1
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Liang Q, Chi G, Cirqueira L, Zhi L, Marasco A, Pilati N, Gunthorpe MJ, Alvaro G, Large CH, Sauer DB, Treptow W, Covarrubias M. The binding and mechanism of a positive allosteric modulator of Kv3 channels. Nat Commun 2024; 15:2533. [PMID: 38514618 PMCID: PMC10957983 DOI: 10.1038/s41467-024-46813-8] [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: 04/10/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Small-molecule modulators of diverse voltage-gated K+ (Kv) channels may help treat a wide range of neurological disorders. However, developing effective modulators requires understanding of their mechanism of action. We apply an orthogonal approach to elucidate the mechanism of action of an imidazolidinedione derivative (AUT5), a highly selective positive allosteric modulator of Kv3.1 and Kv3.2 channels. AUT5 modulation involves positive cooperativity and preferential stabilization of the open state. The cryo-EM structure of the Kv3.1/AUT5 complex at a resolution of 2.5 Å reveals four equivalent AUT5 binding sites at the extracellular inter-subunit interface between the voltage-sensing and pore domains of the channel's tetrameric assembly. Furthermore, we show that the unique extracellular turret regions of Kv3.1 and Kv3.2 essentially govern the selective positive modulation by AUT5. High-resolution apo and bound structures of Kv3.1 demonstrate how AUT5 binding promotes turret rearrangements and interactions with the voltage-sensing domain to favor the open conformation.
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Affiliation(s)
- Qiansheng Liang
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Leonardo Cirqueira
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Lianteng Zhi
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Agostino Marasco
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Nadia Pilati
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Martin J Gunthorpe
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - Giuseppe Alvaro
- Autifony Srl, Istituto di Ricerca Pediatrica Citta' della Speranza, Via Corso Stati Uniti, 4f, 35127, Padua, Italy
| | - Charles H Large
- Autifony Therapeutics, Ltd, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Werner Treptow
- Laboratorio de Biologia Teorica e Computacional, University of Brasilia, Brasilia, Brazil
| | - Manuel Covarrubias
- Department of Neuroscience,, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Jack and Vicki Farber Institute for Neuroscience and the Jefferson Synaptic Biology Center, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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2
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Hao X, Yang Y, Liu J, Zhang D, Ou M, Ke B, Zhu T, Zhou C. The Modulation by Anesthetics and Analgesics of Respiratory Rhythm in the Nervous System. Curr Neuropharmacol 2024; 22:217-240. [PMID: 37563812 PMCID: PMC10788885 DOI: 10.2174/1570159x21666230810110901] [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: 11/23/2022] [Revised: 04/27/2023] [Accepted: 02/28/2023] [Indexed: 08/12/2023] Open
Abstract
Rhythmic eupneic breathing in mammals depends on the coordinated activities of the neural system that sends cranial and spinal motor outputs to respiratory muscles. These outputs modulate lung ventilation and adjust respiratory airflow, which depends on the upper airway patency and ventilatory musculature. Anesthetics are widely used in clinical practice worldwide. In addition to clinically necessary pharmacological effects, respiratory depression is a critical side effect induced by most general anesthetics. Therefore, understanding how general anesthetics modulate the respiratory system is important for the development of safer general anesthetics. Currently used volatile anesthetics and most intravenous anesthetics induce inhibitory effects on respiratory outputs. Various general anesthetics produce differential effects on respiratory characteristics, including the respiratory rate, tidal volume, airway resistance, and ventilatory response. At the cellular and molecular levels, the mechanisms underlying anesthetic-induced breathing depression mainly include modulation of synaptic transmission of ligand-gated ionotropic receptors (e.g., γ-aminobutyric acid, N-methyl-D-aspartate, and nicotinic acetylcholine receptors) and ion channels (e.g., voltage-gated sodium, calcium, and potassium channels, two-pore domain potassium channels, and sodium leak channels), which affect neuronal firing in brainstem respiratory and peripheral chemoreceptor areas. The present review comprehensively summarizes the modulation of the respiratory system by clinically used general anesthetics, including the effects at the molecular, cellular, anatomic, and behavioral levels. Specifically, analgesics, such as opioids, which cause respiratory depression and the "opioid crisis", are discussed. Finally, underlying strategies of respiratory stimulation that target general anesthetics and/or analgesics are summarized.
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Affiliation(s)
- Xuechao Hao
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yaoxin Yang
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jin Liu
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Donghang Zhang
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Mengchan Ou
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Bowen Ke
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Cheng Zhou
- Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital of Sichuan University, Chengdu, 610041, China
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3
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [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: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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Treptow W. Allosteric Modulation of Membrane Proteins by Small Low-Affinity Ligands. J Chem Inf Model 2023; 63:2047-2057. [PMID: 36933226 DOI: 10.1021/acs.jcim.2c01542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Membrane proteins may respond to a variety of ligands under an applied external stimulus. These ligands include small low-affinity molecules that account for functional effects in the mM range. Understanding the modulation of protein function by low-affinity ligands requires characterizing their atomic-level interactions under dilution, challenging the current resolution of theoretical and experimental routines. Part of the problem derives from the fact that small low-affinity ligands may interact with multiple sites of a membrane protein in a highly degenerate manner to a degree that it is better conceived as a partition phenomenon, hard to track at the molecular interface of the protein. Looking for new developments in the field, we rely on the classic two-state Boltzmann model to devise a novel theoretical description of the allosteric modulation mechanism of membrane proteins in the presence of small low-affinity ligands and external stimuli. Free energy stability of the partition process and its energetic influence on the protein coupling with the external stimulus are quantified. The outcome is a simple formulation that allows the description of the equilibrium shifts of the protein in terms of the grand-canonical partition function of the ligand at dilute concentrations. The model's predictions of the spatial distribution and response probability shift across a variety of ligand concentrations, and thermodynamic conjugates can be directly compared to macroscopic measurements, making it especially useful to interpret experimental data at the atomic level. Illustration and discussion of the theory is shown in the context of general anesthetics and voltage-gated channels for which structural data are available.
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Affiliation(s)
- Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília, Distrito Federal, Brasília CEP 70904-970, Brasil
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5
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Roy P, Dennis DG, Eschbach MD, Anand SD, Xu F, Maturano J, Hellman J, Sarlah D, Das A. Metabolites of Cannabigerol Generated by Human Cytochrome P450s Are Bioactive. Biochemistry 2022; 61:2398-2408. [PMID: 36223199 DOI: 10.1021/acs.biochem.2c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The phytocannabinoid cannabigerol (CBG) is the central biosynthetic precursor to many cannabinoids, including Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD). Though the use of CBG has recently witnessed a widespread surge because of its beneficial health effects and lack of psychoactivity, its metabolism by human cytochrome P450s is largely unknown. Herein, we describe comprehensive in vitro and in vivo cytochrome P450 (CYP)-mediated metabolic studies of CBG, ranging from liquid chromatography tandem mass spectrometry-based primary metabolic site determination, synthetic validation, and kinetic behavior using targeted mass spectrometry. These investigations revealed that cyclo-CBG, a recently isolated phytocannabinoid, is the major metabolite that is rapidly formed by selected human cytochrome P450s (CYP2J2, CYP3A4, CYP2D6, CYP2C8, and CYP2C9). Additionally, in vivo studies with mice administered with CBG supported these studies, where cyclo-CBG is the major metabolite as well. Spectroscopic binding studies along with docking and modeling of the CBG molecule near the heme in the active site of P450s confirmed these observations, pointing at the preferred site selectivity of CBG metabolism at the prenyl chain over other positions. Importantly, we found out that CBG and its oxidized CBG metabolites reduced inflammation in BV2 microglial cells stimulated with LPS. Overall, combining enzymological studies, mass spectrometry, and chemical synthesis, we showcase that CBG is rapidly metabolized by human P450s to form oxidized metabolites that are bioactive.
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Affiliation(s)
- Pritam Roy
- Department of Comparative Biosciences, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, Department of Bioengineering, Neuroscience program, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - David G Dennis
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Mark D Eschbach
- Department of Comparative Biosciences, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, Department of Bioengineering, Neuroscience program, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Shravanthi D Anand
- Department of Comparative Biosciences, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, Department of Bioengineering, Neuroscience program, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fengyun Xu
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California 94143, United States
| | - Jonathan Maturano
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Judith Hellman
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California 94143, United States
| | - David Sarlah
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Aditi Das
- Department of Comparative Biosciences, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, Department of Bioengineering, Neuroscience program, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
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6
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Cirqueira L, Stock L, Treptow W. Concentration-Dependent Thermodynamic Analysis of the Partition Process of Small Ligands into Proteins. Comput Struct Biotechnol J 2022; 20:4885-4891. [PMID: 36147679 PMCID: PMC9468351 DOI: 10.1016/j.csbj.2022.08.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/28/2022] Open
Abstract
In the category of functional low-affinity interactions, small ligands may interact with multiple protein sites in a highly degenerate manner. Better conceived as a partition phenomenon at the molecular interface of proteins, such low-affinity interactions appear to be hidden to our current experimental resolution making their structural and functional characterization difficult in the low concentration regime of physiological processes. Characterization of the partition phenomenon under higher chemical forces could be a relevant strategy to tackle the problem provided the results can be scaled back to the low concentration range. Far from being trivial, such scaling demands a concentration-dependent understanding of self-interactions of the ligands, structural perturbations of the protein, among other molecular effects. Accordingly, we elaborate a novel and detailed concentration-dependent thermodynamic analysis of the partition process of small ligands aiming at characterizing the stability and structure of the dilute phenomenon from high concentrations. In analogy to an “aggregate” binding constant of a small molecule over multiple sites of a protein receptor, the model defines the stability of the process as a macroscopic equilibrium constant for the partition number of ligands that can be used to analyze biochemical and functional data of two-component systems driven by low-affinity interactions. Acquisition of such modeling-based structural information is expected to be highly welcome by revealing more traceable protein-binding spots for non-specific ligands.
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7
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Xiao J, Chen Z, Yu B. A Potential Mechanism of Sodium Channel Mediating the General Anesthesia Induced by Propofol. Front Cell Neurosci 2020; 14:593050. [PMID: 33343303 PMCID: PMC7746837 DOI: 10.3389/fncel.2020.593050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
General anesthesia has revolutionized healthcare over the past 200 years and continues to show advancements. However, many phenomena induced by general anesthetics including paradoxical excitation are still poorly understood. Voltage-gated sodium channels (NaV) were believed to be one of the proteins targeted during general anesthesia. Based on electrophysiological measurements before and after propofol treatments of different concentrations, we mathematically modified the Hodgkin–Huxley sodium channel formulations and constructed a thalamocortical model to investigate the potential roles of NaV. The ion channels of individual neurons were modeled using the Hodgkin–Huxley type equations. The enhancement of propofol-induced GABAa current was simulated by increasing the maximal conductance and the time-constant of decay. Electroencephalogram (EEG) was evaluated as the post-synaptic potential from pyramidal (PY) cells. We found that a left shift in activation of NaV was induced primarily by a low concentration of propofol (0.3–10 μM), while a left shift in inactivation of NaV was induced by an increasing concentration (0.3–30 μM). Mathematical simulation indicated that a left shift of NaV activation produced a Hopf bifurcation, leading to cell oscillations. Left shift of NaV activation around a value of 5.5 mV in the thalamocortical models suppressed normal bursting of thalamocortical (TC) cells by triggering its chaotic oscillations. This led to irregular spiking of PY cells and an increased frequency in EEG readings. This observation suggests a mechanism leading to paradoxical excitation during general anesthesia. While a left shift in inactivation led to light hyperpolarization in individual cells, it inhibited the activity of the thalamocortical model after a certain depth of anesthesia. This finding implies that high doses of propofol inhibit the network partly by accelerating NaV toward inactivation. Additionally, this result explains why the application of sodium channel blockers decreases the requirement for general anesthetics. Our study provides an insight into the roles that NaV plays in the mechanism of general anesthesia. Since the activation and inactivation of NaV are structurally independent, it should be possible to avoid side effects by state-dependent binding to the NaV to achieve precision medicine in the future.
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Affiliation(s)
- Jinglei Xiao
- Department of Anesthesiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengguo Chen
- College of Computer, National University of Defence Technology, Changsha, China
| | - Buwei Yu
- Department of Anesthesiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Fukushima Y, Kojima A, Mi X, Ding WG, Kitagawa H, Matsuura H. Open-channel blocking action of volatile anaesthetics desflurane and sevoflurane on human voltage-gated K v 1.5 channel. Br J Pharmacol 2020; 177:3811-3827. [PMID: 32436224 DOI: 10.1111/bph.15105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Volatile anaesthetics have been shown to differentially modulate mammalian Shaker-related voltage-gated potassium (Kv 1.x) channels. This study was designed to investigate molecular and cellular mechanisms underlying the modulatory effects of desflurane or sevoflurane on human Kv 1.5 (hKv 1.5) channels. EXPERIMENTAL APPROACH Thirteen single-point mutations were constructed within pore domain of hKv 1.5 channel using site-directed mutagenesis. The effects of desflurane or sevoflurane on heterologously expressed wild-type and mutant hKv 1.5 channels were examined by whole-cell patch-clamp technique. A computer simulation was conducted to predict the docking pose of desflurane or sevoflurane within hKv 1.5 channel. KEY RESULTS Both desflurane and sevoflurane increased hKv 1.5 current at mild depolarizations but decreased it at strong depolarizations, indicating that these anaesthetics produce both stimulatory and inhibitory actions on hKv 1.5 channels. The inhibitory effect of desflurane or sevoflurane on hKv 1.5 channels arose primarily from its open-channel blocking action. The inhibitory action of desflurane or sevoflurane on hKv 1.5 channels was significantly attenuated in T480A, V505A, and I508A mutant channels, compared with wild-type channel. Computational docking simulation predicted that desflurane or sevoflurane resides within the inner cavity of channel pore and has contact with Thr479, Thr480, Val505, and Ile508. CONCLUSION AND IMPLICATIONS Desflurane and sevoflurane exert an open-channel blocking action on hKv 1.5 channels by functionally interacting with specific amino acids located within the channel pore. This study thus identifies a novel molecular basis mediating inhibitory modulation of hKv 1.5 channels by desflurane and sevoflurane.
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Affiliation(s)
- Yutaka Fukushima
- Department of Physiology, Shiga University of Medical Science, Otsu, Japan.,Department of Anesthesiology, Shiga University of Medical Science, Otsu, Japan
| | - Akiko Kojima
- Department of Anesthesiology, Shiga University of Medical Science, Otsu, Japan
| | - Xinya Mi
- Department of Physiology, Shiga University of Medical Science, Otsu, Japan
| | - Wei-Guang Ding
- Department of Physiology, Shiga University of Medical Science, Otsu, Japan
| | - Hirotoshi Kitagawa
- Department of Anesthesiology, Shiga University of Medical Science, Otsu, Japan
| | - Hiroshi Matsuura
- Department of Physiology, Shiga University of Medical Science, Otsu, Japan
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9
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Malik C, Ghosh S. Quinidine partially blocks mitochondrial voltage-dependent anion channel (VDAC). EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:193-205. [DOI: 10.1007/s00249-020-01426-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023]
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10
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Silva MA, Kiametis AS, Treptow W. Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature. J Chem Inf Model 2020; 60:3463-3471. [PMID: 32096991 DOI: 10.1021/acs.jcim.9b01073] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Donepezil is a second generation acetylcholinesterase (AChE) inhibitor for treatment of Alzheimer's disease (AD). AChE is important for neurotransmission at neuromuscular junctions and cholinergic brain synapses by hydrolyzing acetylcholine into acetate and choline. In vitro data support that donepezil is a reversible, mixed competitive and noncompetitive inhibitor of AChE. The experimental fact then suggests a more complex binding mechanism beyond the molecular view in X-ray models resolved at cryogenic temperatures that show a unique binding mode of donepezil in the active site of the enzyme. Aiming at clarifying the mechanism behind that mixed competitive and noncompetitive nature of the inhibitor, we have applied molecular dynamics (MD) simulations and docking and free-energy calculations to investigate microscopic details and energetics of donepezil association for conditions of substrate-free and -bound states of the enzyme. Liquid-phase MD simulation at room temperature shows AChE transits between "open" and "closed" conformations to control accessibility to the active site and ligand binding. As shown by docking and free-energy calculations, association of donepezil involves its reversible axial displacement and reorientation in the active site of the enzyme, assisted by water molecules. Donepezil binds equally well the main-door anionic binding site PAS, the acyl pocket, and the catalytic site CAS by respectively adopting outward-inward-inward orientations regardless of substrate occupancy-the overall stability of that reaction process depends however on co-occupancy of the enzyme being preferential for its substrate-free state. All together, our findings support a physiologically relevant mechanism of AChE inhibition by donepezil involving multistable interactions modes at the molecular origin of the inhibitor's activity.
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Affiliation(s)
- Monica A Silva
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
| | - Alessandra S Kiametis
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brası́lia DF, Brasília 70910-900, Brasil
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11
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Kiametis A, Stock L, Cirqueira L, Treptow W. Atomistic Model for Simulations of the Sedative Hypnotic Drug 2,2,2-Trichloroethanol. ACS OMEGA 2018; 3:15916-15923. [PMID: 30556017 PMCID: PMC6288786 DOI: 10.1021/acsomega.8b02017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/08/2018] [Indexed: 05/16/2023]
Abstract
2,2,2-Trichloroethanol (TCE) is the active form of the sedative hypnotic drug chloral hydrate, one of the oldest sleep medications in the market. Understanding of TCE's action mechanisms to its many targets, particularly within the ion channel family, could benefit from the state-of-the-art computational molecular studies. In this direction, we employed de novo modeling aided by the force field toolkit to develop CHARMM36-compatible TCE parameters. The classical potential energy function was calibrated targeting molecular conformations, local interactions with water molecules, and liquid bulk properties. Reference data comes from both tabulated thermodynamic properties and ab initio calculations at the MP2 level. TCE solvation free energy calculations in water and oil reproduce a lipophilic, yet nonhydrophobic, behavior. Indeed, the potential mean force profile for TCE partition through the phospholipid bilayer reveals the sedative's preference for the interfacial region. The calculated partition coefficient also matches experimental measures. Further validation of the proposed parameters is supported by the model's ability to recapitulate quenching experiments demonstrating TCE binding to bovine serum albumin.
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12
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Stock L, Hosoume J, Cirqueira L, Treptow W. Binding of the general anesthetic sevoflurane to ion channels. PLoS Comput Biol 2018; 14:e1006605. [PMID: 30475796 PMCID: PMC6283617 DOI: 10.1371/journal.pcbi.1006605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/06/2018] [Accepted: 10/26/2018] [Indexed: 11/21/2022] Open
Abstract
The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia. Despite advancements in the field, a first principle all-atom demonstration of this structure-function premise is still missing. We focus on the clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds protein’s well-characterized open and closed structures in a conformation-dependent manner to shift channel equilibrium. We employ an innovative approach relying on extensive docking calculations and free-energy perturbation of all potential binding sites revealed by the latter, and find sevoflurane binds open and closed structures at multiple sites under complex saturation and concentration effects. Results point to a non-trivial interplay of site and conformation-dependent modes of action involving distinct binding sites that increase channel open-probability at diluted ligand concentrations. Given the challenge in exploring more complex processes potentially impacting channel-anesthetic interaction, the result is revealing as it demonstrates the process of multiple anesthetic binding events alone may account for open-probability shifts recorded in measurements. General anesthetics are central to modern medicine, yet their microscopic mechanism of action is still unknown. Here, we demonstrate that a clinically used anesthetic, sevoflurane, binds the mammalian voltage-gated potassium channel Kv1.2 effecting a shift in its open probability, even at low concentrations. The results, supported by recent experimental measurements, are promising as they demonstrate that the molecular process of direct binding of anesthetic to ion channels play a relevant role in anesthesia.
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Affiliation(s)
- Letícia Stock
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Juliana Hosoume
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Leonardo Cirqueira
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
| | - Werner Treptow
- Laboratório de Biologia Teórica e Computacional (LBTC), Universidade de Brasília DF, Brasil
- * E-mail:
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Oakes V, Domene C. Capturing the Molecular Mechanism of Anesthetic Action by Simulation Methods. Chem Rev 2018; 119:5998-6014. [DOI: 10.1021/acs.chemrev.8b00366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Victoria Oakes
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Carmen Domene
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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14
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Jorgensen C, Domene C. Location and Character of Volatile General Anesthetics Binding Sites in the Transmembrane Domain of TRPV1. Mol Pharm 2018; 15:3920-3930. [PMID: 30067911 DOI: 10.1021/acs.molpharmaceut.8b00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It has been proposed that general anesthesia results from direct multisite interactions with multiple and diverse ion channels in the brain. An understanding of the mechanisms by which general anesthetics modulate ion channels is essential to clarify their underlying behavior and their role in reversible immobilization and amnesia. Despite the fact that volatile general anesthetics are drugs that primarily induce insensitivity to pain, they have been reported to sensitize and active the vanilloid-1 receptor, TRPV1, which is known to mediate the response of the nervous system to certain harmful stimuli and which plays a crucial role in the pain pathway. Currently, the mechanism of action of anesthetics is unknown and the precise molecular sites of interaction have not been identified. Here, using ∼2.5 μs of classical molecular dynamics simulations and metadynamics, we explore these enigmas. Binding sites are identified and the strength of the association is further characterized using alchemical free-energy calculations. Anesthetic binding/unbinding proceeds primarily through a membrane-embedded pathway, and subsequently, a complex scenario is established involving multiple binding sites featuring single or multiple occupancy states of two small volatile drugs. One of the five anesthetic binding sites reported was previously identified experimentally, and another one, importantly, is identical to that of capsaicin, one of the chemical stimuli that activate TRPV1. However, in contrast to capsaicin, isoflurane and chloroform binding free-energies render modest to no association compared to capsaicin, suggesting a different activation mechanism. Uncovering chloroform and isoflurane modulatory sites will further our understanding of the TRPV1 molecular machinery and open the possibility of developing site-specific drugs.
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Affiliation(s)
- Christian Jorgensen
- Department of Chemistry , King's College London , Britannia House, 7 Trinity Street , London SE1 1DB , U.K
| | - Carmen Domene
- Department of Chemistry , King's College London , Britannia House, 7 Trinity Street , London SE1 1DB , U.K.,Department of Chemistry , University of Bath , 1 South Building, Claverton Down , Bath BA2 7AY , U.K.,Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford OX1 3TA , U.K
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Yang E, Zhi L, Liang Q, Covarrubias M. Electrophysiological Analysis of Voltage-Gated Ion Channel Modulation by General Anesthetics. Methods Enzymol 2018; 602:339-368. [PMID: 29588038 DOI: 10.1016/bs.mie.2018.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Voltage-gated ion channels (VGICs) of excitable tissues are emerging as targets likely involved in both the therapeutic and toxic effects of inhaled and intravenous general anesthetics. Whereas sevoflurane and propofol inhibit voltage-gated Na+ channels (Navs), sevoflurane potentiates certain voltage-gated K+ channels (Kvs). The combination of these effects would dampen neural excitability and, therefore, might contribute to the clinical endpoints of general anesthesia. As the body of work regarding the interaction of general anesthetics with VGICs continues to grow, a multidisciplinary approach involving functional, biochemical, structural, and computational techniques, many of which are detailed in other chapters, has increasingly become necessary to solve the molecular mechanism of general anesthetic action on VGICs. Here, we focus on electrophysiological and modeling approaches and methodologies to describe how our work has elucidated the biophysical basis of the inhibition Navs by propofol and the potentiation of Kvs by sevoflurane.
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Affiliation(s)
- Elaine Yang
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States.
| | - Lianteng Zhi
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
| | - Qiansheng Liang
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
| | - Manuel Covarrubias
- Vickie and Jack Farber Institute for Neuroscience, Sidney Kimmel Medical College, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, United States
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