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Joseph TT, Bu W, Lin W, Zoubak L, Yeliseev A, Liu R, Eckenhoff RG, Brannigan G. Ketamine Metabolite (2 R,6 R)-Hydroxynorketamine Interacts with μ and κ Opioid Receptors. ACS Chem Neurosci 2021; 12:1487-1497. [PMID: 33905229 PMCID: PMC8154314 DOI: 10.1021/acschemneuro.0c00741] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
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Ketamine is an anesthetic,
analgesic, and antidepressant whose
secondary metabolite (2R,6R)-hydroxynorketamine
(HNK) has N-methyl-d-aspartate-receptor-independent
antidepressant activity in a rodent model. In humans, naltrexone attenuates
its antidepressant effect, consistent with opioid pathway involvement.
No detailed biophysical description is available of opioid receptor
binding of ketamine or its metabolites. Using molecular dynamics simulations
with free energy perturbation, we characterize the binding site and
affinities of ketamine and metabolites in μ and κ opioid
receptors, finding a profound effect of the protonation state. G-protein
recruitment assays show that HNK is an inverse agonist, attenuated
by naltrexone, in these receptors with IC50 values congruous
with our simulations. Overall, our findings are consistent with opioid
pathway involvement in ketamine function.
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Affiliation(s)
- Thomas T. Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Weiming Bu
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wenzhen Lin
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Molecular Biology, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Lioudmila Zoubak
- National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Alexei Yeliseev
- National Institute of Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20852, United States
| | - Renyu Liu
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Roderic G. Eckenhoff
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University, Camden, New Jersey 08102, United States
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Tikhonova TA, Rassokhina IV, Kondrakhin EA, Fedosov MA, Bukanova JV, Rossokhin AV, Sharonova IN, Kovalev GI, Zavarzin IV, Volkova YA. Development of 1,3-thiazole analogues of imidazopyridines as potent positive allosteric modulators of GABA A receptors. Bioorg Chem 2019; 94:103334. [PMID: 31711764 DOI: 10.1016/j.bioorg.2019.103334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/17/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022]
Abstract
Structure-activity relationship studies were conducted in the search for 1,3-thiazole isosteric analogs of imidazopyridine drugs (Zolpidem, Alpidem). Three series of novel γ-aminobutyric acid receptor (GABAAR) ligands belonging to imidazo[2,1-b]thiazoles, imidazo[2,1-b][1,3,4]thiadiazoles, and benzo[d]imidazo[2,1-b]thiazoles were synthesized and characterized as active agents against GABAAR benzodiazepine-binding site. In each of these series, potent compounds were discovered using a radioligand competition binding assay. The functional properties of highest-affinity compounds 28 and 37 as GABAAR positive allosteric modulators (PAMs) were determined by electrophysiological measurements. In vivo studies on zebrafish demonstrated their potential for the further development of anxiolytics. Using the OECD "Fish, Acute Toxicity Test" active compounds were found safe and non-toxic. Structural bases for activity of benzo[d]imidazo[2,1-b]thiazoles were proposed using molecular docking studies. The isosteric replacement of the pyridine nuclei by 1,3-thiazole, 1,3,4-thiadiazole, or 1,3-benzothiazole in the ring-fused imidazole class of GABAAR PAMs was shown to be promising for the development of novel hypnotics, anxiolytics, anticonvulsants, and sedatives drug-candidates.
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Affiliation(s)
- Tatyana A Tikhonova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russia
| | - Irina V Rassokhina
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russia
| | - Eugeny A Kondrakhin
- V. V. Zakusov Institute of Pharmacology, Russian Academy of Sciences, 8 Baltiyskaya Str., 125315 Moscow, Russia
| | - Mikhail A Fedosov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russia
| | - Julia V Bukanova
- Research Center of Neurology, 5 By-str. Obukha, 105064 Moscow, Russia
| | | | - Irina N Sharonova
- Research Center of Neurology, 5 By-str. Obukha, 105064 Moscow, Russia
| | - Georgy I Kovalev
- V. V. Zakusov Institute of Pharmacology, Russian Academy of Sciences, 8 Baltiyskaya Str., 125315 Moscow, Russia
| | - Igor V Zavarzin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russia
| | - Yulia A Volkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russia.
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Abstract
Anesthetic drug molecules are being increasingly studied through the use of computational methods such as molecular dynamics (MD). Molecular mechanics force fields require the investigator to supply parameters for the force field equation, which are not available for novel molecules. Careful selection of these parameters is critical for simulations to produce meaningful results. Therefore, this chapter presents a state-of-the-art method for determining these parameters by comparison to quantum mechanics calculations and experimental quantities. Ketamine is used as an example to demonstrate the process.
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Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M. Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State. J Biol Chem 2016; 292:1550-1558. [PMID: 27986812 DOI: 10.1074/jbc.m116.766964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/06/2016] [Indexed: 12/12/2022] Open
Abstract
Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized, and these derivatives helped us unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturate inhibition of cationic pLGICs and allows the rationalization of several structural and functional features previously observed for barbiturates.
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Affiliation(s)
- Zaineb Fourati
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Reinis Reinholds Ruza
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France
| | - Duncan Laverty
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Emmanuelle Drège
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Sandrine Delarue-Cochin
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Delphine Joseph
- the UMR 8076 du CNRS, BioCIS, Faculté de Pharmacie, Université Paris Sud, 92296 Chatenay-Malabry, France
| | - Patrice Koehl
- the Department of Computer Science, University of California, Davis, California 95616
| | - Trevor Smart
- the Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom.
| | - Marc Delarue
- From the Unité de Dynamique Structurale des Macromolécules, UMR 3528 du CNRS, Institut Pasteur, 75015 Paris, France.
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Discovery of allosteric modulators for GABAA receptors by ligand-directed chemistry. Nat Chem Biol 2016; 12:822-30. [DOI: 10.1038/nchembio.2150] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia. Anesthesiology 2014; 121:1018-27. [DOI: 10.1097/aln.0000000000000435] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Background:
The mechanisms by which general anesthetics, including xenon and nitrous oxide, act are only beginning to be discovered. However, structural approaches revealed weak but specific protein–gas interactions.
Methods:
To improve knowledge, we performed x-ray crystallography studies under xenon and nitrous oxide pressure in a series of 10 binding sites within four proteins.
Results:
Whatever the pressure, we show (1) hydrophobicity of the gas binding sites has a screening effect on xenon and nitrous oxide binding, with a threshold value of 83% beyond which and below which xenon and nitrous oxide, respectively, binds to their sites preferentially compared to each other; (2) xenon and nitrous oxide occupancies are significantly correlated respectively to the product and the ratio of hydrophobicity by volume, indicating that hydrophobicity and volume are binding parameters that complement and oppose each other’s effects; and (3) the ratio of occupancy of xenon to nitrous oxide is significantly correlated to hydrophobicity of their binding sites.
Conclusions:
These data demonstrate that xenon and nitrous oxide obey different binding mechanisms, a finding that argues against all unitary hypotheses of narcosis and anesthesia, and indicate that the Meyer–Overton rule of a high correlation between anesthetic potency and solubility in lipids of general anesthetics is often overinterpreted. This study provides evidence that the mechanisms of gas binding to proteins and therefore of general anesthesia should be considered as the result of a fully reversible interaction between a drug ligand and a receptor as this occurs in classical pharmacology.
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Barbituric acids as a useful tool for the construction of coordination and supramolecular compounds. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.01.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Lin L, Lv J, Ji Y, Feng J, Liu Y, Wang Z, Zhang W. Characterization of Barbiturates by Infrared and Raman Microscopy. ANAL LETT 2013. [DOI: 10.1080/00032719.2013.816964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Xu L, Matsunaga F, Xi J, Li M, Ma J, Liu R. n-Dodecyl β-D-maltoside specifically competes with general anesthetics for anesthetic binding sites. J Biomol Struct Dyn 2013; 32:1833-40. [PMID: 24063524 DOI: 10.1080/07391102.2013.838699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We recently demonstrated that the anionic detergent sodium dodecyl sulfate (SDS) specifically interacts with the anesthetic binding site in horse spleen apoferritin, a soluble protein which models anesthetic binding sites in receptors. This raises the possibility of other detergents similarly interacting with and occluding such sites from anesthetics, thereby preventing the proper identification of novel anesthetic binding sites. n-Dodecyl β-D-maltoside (DDM) is a non-ionic detergent commonly used during protein-anesthetic studies because of its mild and non-denaturing properties. In this study, we demonstrate that SDS and DDM occupy anesthetic binding sites in the model proteins human serum albumin (HSA) and horse spleen apoferritin and thereby inhibit the binding of the general anesthetics propofol and isoflurane. DDM specifically interacts with HSA (Kd = 40 μM) with a lower affinity than SDS (Kd = 2 μM). DDM exerts all these effects while not perturbing the native structures of either model protein. Computational calculations corroborated the experimental results by demonstrating that the binding sites for DDM and both anesthetics on the model proteins overlapped. Collectively, our results indicate that DDM and SDS specifically interact with anesthetic binding sites and may thus prevent the identification of novel anesthetic sites. Special precaution should be taken when undertaking and interpreting results from protein-anesthetic investigations utilizing detergents like SDS and DDM.
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Affiliation(s)
- Longhe Xu
- a Department of Anesthesiology and Critical Care , Perelman School of Medicine at the University of Pennsylvania , 336 John Morgan Building, 3620 Hamilton Walk, Philadelphia , PA , USA
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Chitilian HV, Eckenhoff RG, Raines DE. Anesthetic drug development: Novel drugs and new approaches. Surg Neurol Int 2013; 4:S2-S10. [PMID: 23653886 PMCID: PMC3642742 DOI: 10.4103/2152-7806.109179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/08/2012] [Indexed: 12/17/2022] Open
Abstract
The ideal sedative–hypnotic drug would be a rapidly titratable intravenous agent with a high therapeutic index and minimal side effects. The current efforts to develop such agents are primarily focused on modifying the structures of existing drugs to improve their pharmacodynamic and pharmacokinetic properties. Drugs currently under development using this rational design approach include analogues of midazolam, propofol, and etomidate, such as remimazolam, PF0713, and cyclopropyl methoxycarbonyl-etomidate (MOC-etomidate), respectively. An alternative approach involves the rapid screening of large libraries of molecules for activity in structural or phenotypic assays that approximate anesthetic and target receptor interactions. Such high-throughput screening offers the potential for identifying completely novel classes of drugs. Anesthetic drug development is experiencing a resurgence of interest because there are new demands on our clinical practice that can be met, at least in part, with better agents. The goal of this review is to provide the reader with a glimpse of the novel anesthetic drugs and new developmental approaches that lie on the horizon.
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Affiliation(s)
- Hovig V Chitilian
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
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