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Seto T. General anesthetic binding mode via hydration with weak affinity and molecular discrimination: General anesthetic dissolution in interfacial water of the common binding site of GABA A receptor. Biophys Physicobiol 2023; 20:e200005. [PMID: 38496235 PMCID: PMC10941959 DOI: 10.2142/biophysico.bppb-v20.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
The GABAA receptor (GABAAR) is a target channel for the loss of awareness of general anesthesia. General anesthetic (GA) spans a wide range of chemical structures, such as monatomic molecules, barbital acids, phenols, ethers, and alkanes. GA has a weak binding affinity, and the affinity has a characteristic that correlates with the solubility in olive oil rather than the molecular shape. The GA binding site of GABAAR is common to GAs and exists in the transmembrane domain of the GABAAR intersubunit. In this study, the mechanism of GA binding, which allows binding of various GAs with intersubunit selectivity, was elucidated from the hydration analysis of the binding site. Regardless of the diverse GA chemical structures, a strong correlation was observed between the binding free energy and total dehydration number of the binding process. The GA binding free energy was more involved in the binding dehydration and showed molecular recognition that allowed for the binding of various GA structures via binding site hydration. We regarded the GA substitution for the interfacial water molecule of the binding site as a dissolution into the interfacial hydration layer. The elucidation of the GA binding mechanism mediated by hydration at the GABAAR common binding site provides a rationale for the combined use of anesthetics in medical practice and its combination adjustments via drug interactions.
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Affiliation(s)
- Tomoyoshi Seto
- Department of Anesthesiology, School of Medicine, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
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Chattaraj R, Hwang M, Zemerov SD, Dmochowski IJ, Hammer DA, Lee D, Sehgal CM. Ultrasound Responsive Noble Gas Microbubbles for Applications in Image-Guided Gas Delivery. Adv Healthc Mater 2020; 9:e1901721. [PMID: 32207250 PMCID: PMC7457952 DOI: 10.1002/adhm.201901721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 12/18/2022]
Abstract
Noble gases, especially xenon (Xe), have been shown to have antiapoptotic effects in treating hypoxia ischemia related injuries. Currently, in vivo gas delivery is systemic and performed through inhalation, leading to reduced efficacy at the injury site. This report provides a first demonstration of the encapsulation of pure Xe, Ar, or He in phospholipid-coated sub-10 µm microbubbles, without the necessity of stabilizing perfluorocarbon additives. Optimization of shell compositions and preparation techniques show that distearoylphosphatidylcholine (DSPC) with DSPE-PEG5000 can produce stable microbubbles upon shaking, while dibehenoylphosphatidylcholine (DBPC) blended with either DSPE-PEG2000 or DSPE-PEG5000 produces a high yield of microbubbles via a sonication/centrifugation method. Xe and Ar concentrations released into the microbubble suspension headspace are measured using GC-MS, while Xe released directly in solution is detected by the fluorescence quenching of a Xe-sensitive cryptophane molecule. Bubble production is found to be amenable to scale-up while maintaining their size distribution and stability. Excellent ultrasound contrast is observed in a phantom for several minutes under physiological conditions, while an intravenous administration of a bolus of pure Xe microbubbles provides significant contrast in a mouse in pre- and post-lung settings (heart and kidney, respectively), paving the way for image-guided, localized gas delivery for theranostic applications.
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Affiliation(s)
- Rajarshi Chattaraj
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Misun Hwang
- Department of Radiology, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania 19104, United States; Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Serge D. Zemerov
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniel A. Hammer
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chandra M. Sehgal
- Department of Radiology, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania 19104, United States
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Winkler DA, Katz I, Farjot G, Warden AC, Thornton AW. Decoding the Rich Biological Properties of Noble Gases: How Well Can We Predict Noble Gas Binding to Diverse Proteins? ChemMedChem 2018; 13:1931-1938. [PMID: 30003691 DOI: 10.1002/cmdc.201800434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/19/2022]
Abstract
The chemically inert noble gases display a surprisingly rich spectrum of useful biological properties. Relatively little is known about the molecular mechanisms behind these effects. It is clearly not feasible to conduct large numbers of pharmacological experiments on noble gases to identify activity. Computational studies of the binding of noble gases and proteins can address this paucity of information and provide insight into mechanisms of action. We used bespoke computational grid calculations to predict the positions of energy minima in the interactions of noble gases with diverse proteins. The method was validated by quantifying how well simulations could predict binding positions in 131 diverse protein X-ray structures containing 399 Xe and Kr atoms. We found excellent agreement between calculated and experimental binding positions of noble gases. 94 % of all crystallographic xenon atoms were within 1 Xe van der Waals (vdW) diameter of a predicted binding site, and 97 % lay within 2 vdW diameters. 100 % of crystallographic krypton atoms were within 1 Kr vdW diameter of a predicted binding site. We showed the feasibility of large-scale computational screening of all ≈60 000 unique structures in the Protein Data Bank. This will elucidate biochemical mechanisms by which these novel 'atomic drugs' elicit their valuable biochemical properties and identify new medical uses.
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Affiliation(s)
- David A Winkler
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
- Biochemistry and Genetics, La Trobe University, Kingsbury Drive, Bundoora, 3086, Australia
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, 3052, Australia
| | - Ira Katz
- Early Drug Development, Air Liquide Santé International, Centre de Recherche Paris-Saclay, Jouy-en-Josas, France
- Department of Mechanical Engineering, Lafayette College, Easton, PA, USA
| | - Géraldine Farjot
- Early Drug Development, Air Liquide Santé International, Centre de Recherche Paris-Saclay, Jouy-en-Josas, France
| | - Andrew C Warden
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
| | - Aaron W Thornton
- Manufacturing Business Unit, CSIRO, Bayview Avenue, Clayton, 3168, Australia
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Nishijima M, Pace TC, Bohne C, Mori T, Inoue Y, Wada T. Highly enantiodifferentiating site of human serum albumin for mediating photocyclodimerization of 2-anthracenecarboxylate elucidated by site-specific inhibition/quenching with xenon. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. PLoS One 2016; 11:e0149795. [PMID: 26910105 PMCID: PMC4765991 DOI: 10.1371/journal.pone.0149795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022] Open
Abstract
GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.
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Affiliation(s)
- Ludovic Sauguet
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Zeineb Fourati
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Thierry Prangé
- Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
- * E-mail:
| | - Nathalie Colloc'h
- CNRS, UMR 6301, ISTCT CERVOxy group, GIP Cyceron, Caen, France
- UNICAEN, Normandie Univ., UMR 6301 ISTCT, Caen, France
- CEA, DSV/I2BM, UMR 6301 ISTCT, Caen, France
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Qiu L, Lin J, Bertaccini EJ. Insights into the Nature of Anesthetic-Protein Interactions: An ONIOM Study. J Phys Chem B 2015; 119:12771-82. [PMID: 26388288 DOI: 10.1021/acs.jpcb.5b05897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anesthetics have been employed widely to relieve surgical suffering, but their mechanism of action is not yet clear. For over a century, the mechanism of anesthesia was previously thought to be via lipid bilayer interactions. In the present work, a rigorous three-layer ONIOM(M06-2X/6-31+G*:PM6:AMBER) method was utilized to investigate the nature of interactions between several anesthetics and actual protein binding sites. According to the calculated structural features, interaction energies, atomic charges, and electrostatic potential surfaces, the amphiphilic nature of anesthetic-protein interactions was demonstrated for both inhalational and injectable anesthetics. The existence of hydrogen and halogen bonding interactions between anesthetics and proteins was clearly identified, and these interactions served to assist ligand recognition and binding by the protein. Within all complexes of inhalational or injectable anesthetics, the polarization effects play a dominant role over the steric effects and induce a significant asymmetry in the otherwise symmetric atomic charge distributions of the free ligands in vacuo. This study provides new insight into the mechanism of action of general anesthetics in a more rigorous way than previously described. Future rational design of safer anesthetics for an aging and more physiologically vulnerable population will be predicated on this greater understanding of such specific interactions.
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Affiliation(s)
- Ling Qiu
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China.,Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China
| | - Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
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Moskovitz Y, Yang H. Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers. SOFT MATTER 2015; 11:2125-2138. [PMID: 25612767 DOI: 10.1039/c4sm02667e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules in the pressure range of 1-1000 bar and at a temperature of 310 K. Xenon and argon have been tested as model gases for general anaesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremors in hyperbaric conditions. The analysis of stacked radial pair distribution functions of DOPC headgroup atoms revealed the explicit solvation potential of the gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor, while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar order parameter patterns for both DOPC acyl chains, which are opposite of the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the 'critical volume' hypothesis of anaesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1-100 bar could be associated with the possible manifestation of neurological tremors at the atomic scale. The non-immobiliser neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing the monolayer undulation rate, which indicates that enhanced diffusivity rather than atomic size is the key factor.
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Affiliation(s)
- Yevgeny Moskovitz
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37130, USA
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Wołoszyn Ł, Ilczyszyn M, Ilczyszyn MM. Experimental evidence on interaction between xenon and bovine serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 125:449-452. [PMID: 24613623 DOI: 10.1016/j.saa.2014.02.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/29/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
Xenon gas interacts with bovine serum albumin (BSA) dissolved in a physiological buffer solution. The fluorescence quenching related to the Trp emission is reversible and depends linearly on the time of saturation by Xe. The most probable site of this interaction is Trp212. The common emission of all BSA fluorophores is also influenced by Xe but this quenching is more complex and suggests: (i) at least two sites occupied by Xe and related to the Tyr and Trp residues; (ii) structural variations of BSA induced by the Xe guest atoms.
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Affiliation(s)
- Łukasz Wołoszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383 Wrocław, Poland
| | - Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383 Wrocław, Poland.
| | - Maria M Ilczyszyn
- Faculty of Chemistry, Wrocław University, Joliot Curie 14, 50-383 Wrocław, Poland
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Fujiwara SI, Amisaki T. Fatty acid binding to serum albumin: Molecular simulation approaches. Biochim Biophys Acta Gen Subj 2013; 1830:5427-34. [DOI: 10.1016/j.bbagen.2013.03.032] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 02/02/2023]
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Ye Z, Zhang R, Sun X. Bustling argon: biological effect. Med Gas Res 2013; 3:22. [PMID: 24088583 PMCID: PMC3850710 DOI: 10.1186/2045-9912-3-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/27/2013] [Indexed: 12/24/2022] Open
Abstract
Argon is a noble gas in group 18 of the periodic table. Certificated to exist in air atmosphere merely one century ago, discovery of argon shows interesting stories of researching and exploring. It was assumed to have no chemical activity. However, argon indeed present its biological effect on mammals. Narcotic effect of argon in diving operation and neur-protective function of argon in cerebral injury demonstrate that argon has crucial effect and be concentrated on is necessary. Furthermore, consider to be harmless to human, argon clinical application in therapy would be another option.
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Affiliation(s)
- Zhouheng Ye
- Department of Diving Medicine, Second Military Medical University, Shanghai 200433, China.
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Andriichenko NN, Ermilov AY. Using the DFT-D method to describe dispersion interactions in systems of weakly-bonded Xe-aromatic molecules. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413080062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gąszowski D, Ilczyszyn M. Hydrogen bonding to xenon: A comparison with neon, argon and krypton complexes. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.11.083] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ilczyszyn M, Selent M, Ilczyszyn MM. Participation of Xenon Guest in Hydrogen Bond Network of β-Hydroquinone Crystal. J Phys Chem A 2012; 116:3206-14. [DOI: 10.1021/jp210670k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Ilczyszyn
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
| | - Marcin Selent
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
- Department of Physics, University of Oulu, 90014 Oulu, Finland
| | - Maria M. Ilczyszyn
- Faculty of Chemistry, Wrocław University, 50-383 Wrocław,
Joliot Curie 14, Poland
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Rizvi M, Jawad N, Li Y, Vizcaychipi MP, Maze M, Ma D. Effect of noble gases on oxygen and glucose deprived injury in human tubular kidney cells. Exp Biol Med (Maywood) 2010; 235:886-91. [PMID: 20472713 DOI: 10.1258/ebm.2010.009366] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The noble gas xenon has been shown to be protective in preconditioning settings against renal ischemic injury. The aims of this study were to determine the protective effects of the other noble gases, helium, neon, argon, krypton and xenon, on human tubular kidney HK2 cells in vitro. Cultured human renal tubular cells (HK2) were exposed to noble gas preconditioning (75% noble gas; 20% O(2); 5% CO(2)) for three hours or mock preconditioning. Twenty-four hours after gas exposure, cell injury was provoked with oxygen-glucose deprived (OGD) culture medium for three hours. Cell viability was assessed 24 h post-OGD by a 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide assay. Other cohorts of cultured cells were incubated in the absence of OGD in 75% noble gas, 20% O(2) and 5% CO(2) and cellular signals phospho-Akt (p-Akt), hypoxia-inducible factor-1alpha (HIF-1alpha) and Bcl-2 were assessed by Western blotting. OGD caused a reduction in cell viability to 0.382 +/- 0.1 from 1.0 +/- 0.15 at control (P < 0.01). Neon, argon and krypton showed no protection from injury (0.404 +/- 0.03; 0.428 +/- 0.02; 0.452 +/- 0.02; P > 0.05). Helium by comparison significantly enhanced cell injury (0.191 +/- 0.05; P < 0.01). Xenon alone exerted a protective effect (0.678 +/- 0.07; P < 0.001). In the absence of OGD, helium was also detrimental (0.909 +/- 0.07; P < 0.01). Xenon caused an increased expression of p-Akt, HIF-1alpha and Bcl-2, while the other noble gases did not modify protein expression. These results suggest that unlike other noble gases, preconditioning with the anesthetic noble gas xenon may have a role in protection against renal ischemic injury.
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Affiliation(s)
- Maleeha Rizvi
- Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK
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