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Maciag M, Plazinski W, Pulawski W, Kolinski M, Jozwiak K, Plazinska A. A comprehensive pharmacological analysis of fenoterol and its derivatives to unravel the role of β 2-adrenergic receptor in zebrafish. Biomed Pharmacother 2023; 160:114355. [PMID: 36739761 DOI: 10.1016/j.biopha.2023.114355] [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: 11/08/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
β-adrenergic receptors (βARs) belong to a key molecular targets that regulate the most important processes occurring in the human organism. Although over the last decades a zebrafish model has been developed as a model complementary to rodents in biomedical research, the role of β2AR in regulation of pathological and toxicological effects remains to elucidate. Therefore, the study aimed to clarify the role of β2AR with a particular emphasis on the distinct role of subtypes A and B of zebrafish β2AR. As model compounds selective β2AR agonists - (R,R)-fenoterol ((R,R)-Fen) and its new derivatives: (R,R)-4'-methoxyfenoterol ((R,R)-MFen) and (R,R)-4'-methoxy-1-naphtylfenoterol ((R,R)-MNFen) - were tested. We described dose-dependent changes observed after fenoterols exposure in terms of general toxicity, cardiotoxicity and neurobehavioural responses. Subsequently, to better characterise the role of β2-adrenergic stimulation in zebrafish, we have performed a series of molecular docking simulations. Our results indicate that (R,R)-Fen displays the highest affinity for subtype A of zebrafish β2AR and β2AAR might be involved in pigment depletion. (R,R)-MFen shows the lowest affinity for zebrafish β2ARs out of the tested fenoterols and this might be associated with its cardiotoxic and anxiogenic effects. (R,R)-MNFen displays the highest affinity for subtype B of zebrafish β2AR and modulation of this receptor might be associated with the development of malformations, increases locomotor activity and induces a negative chronotropic effect. Taken together, the presented data offer insights into the functional responses of the zebrafish β2ARs confirming their intraspecies conservation, and support the translation of the zebrafish model in pharmacological and toxicological research.
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Affiliation(s)
- Monika Maciag
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Independent Laboratory of Behavioral Studies, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
| | - Wojciech Plazinski
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 8 Niezapominajek Street, 30-239 Cracow, Poland
| | - Wojciech Pulawski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Krzysztof Jozwiak
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
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Han Y, Dawson JRD, DeMarco KR, Rouen KC, Bekker S, Yarov-Yarovoy V, Clancy CE, Xiang YK, Vorobyov I. Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein. Proc Natl Acad Sci U S A 2023; 120:e2215916120. [PMID: 36853938 PMCID: PMC10013855 DOI: 10.1073/pnas.2215916120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest group of membrane receptors for transmembrane signal transduction. Ligand-induced activation of GPCRs triggers G protein activation followed by various signaling cascades. Understanding the structural and energetic determinants of ligand binding to GPCRs and GPCRs to G proteins is crucial to the design of pharmacological treatments targeting specific conformations of these proteins to precisely control their signaling properties. In this study, we focused on interactions of a prototypical GPCR, beta-2 adrenergic receptor (β2AR), with its endogenous agonist, norepinephrine (NE), and the stimulatory G protein (Gs). Using molecular dynamics (MD) simulations, we demonstrated the stabilization of cationic NE, NE(+), binding to β2AR by Gs protein recruitment, in line with experimental observations. We also captured the partial dissociation of the ligand from β2AR and the conformational interconversions of Gs between closed and open conformations in the NE(+)-β2AR-Gs ternary complex while it is still bound to the receptor. The variation of NE(+) binding poses was found to alter Gs α subunit (Gsα) conformational transitions. Our simulations showed that the interdomain movement and the stacking of Gsα α1 and α5 helices are significant for increasing the distance between the Gsα and β2AR, which may indicate a partial dissociation of Gsα The distance increase commences when Gsα is predominantly in an open state and can be triggered by the intracellular loop 3 (ICL3) of β2AR interacting with Gsα, causing conformational changes of the α5 helix. Our results help explain molecular mechanisms of ligand and GPCR-mediated modulation of G protein activation.
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Affiliation(s)
- Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - John R. D. Dawson
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - Kyle C. Rouen
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Science and Engineering, American River College, Sacramento, CA95841
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA95616
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
| | - Yang K. Xiang
- Department of Pharmacology, University of California, Davis, CA95616
- VA Northern California Health Care System, Mather, CA95655
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
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L-DOPA and Droxidopa: From Force Field Development to Molecular Docking into Human β2-Adrenergic Receptor. Life (Basel) 2022; 12:life12091393. [PMID: 36143429 PMCID: PMC9501711 DOI: 10.3390/life12091393] [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: 06/29/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to β2-adrenergic receptor (β2AR) inactive and active states has led us to investigate protein–ligand interactions using molecular docking calculations. To perform this study, the 3.2 Å X-ray crystal structure of the active conformation of human β2AR in the complex with the endogenous agonist adrenaline has been used as a template for investigating the binding of two exogenous catecholamines to this adrenergic receptor. Here, we show the derivation of L-DOPA and Droxidopa OPLS all atom (AA) force field (FF) parameters via quantum mechanical (QM) calculations, molecular dynamics (MD) simulations in aqueous solutions of the two catecholamines and the molecular docking of both ligands into rigid and flexible β2AR models. We observe that both ligands share with adrenaline similar experimentally observed binding anchor sites, which are constituted by Asp113/Asn312 and Ser203/Ser204/Ser207 side chains. Moreover, both L-DOPA and Droxidopa molecules exhibit binding affinities comparable to that predicted for adrenaline, which is in good agreement with previous experimental and computational results. L-DOPA and Droxidopa OPLS AA FFs have also been tested by performing MD simulations of these ligands docked into β2AR proteins embedded in lipid membranes. Both hydrogen bonds and hydrophobic interaction networks observed over the 1 μs MD simulation are comparable with those derived from molecular docking calculations and MD simulations performed with the CHARMM FF.
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Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
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Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
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Sykes DA, Jiménez‐Rosés M, Reilly J, Fairhurst RA, Charlton SJ, Veprintsev DB. Exploring the kinetic selectivity of drugs targeting the β 1 -adrenoceptor. Pharmacol Res Perspect 2022; 10:e00978. [PMID: 35762357 PMCID: PMC9237807 DOI: 10.1002/prp2.978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
In this study, we report the β1 -adrenoceptor binding kinetics of several clinically relevant β1/2 -adrenoceptor (β1/2 AR) agonists and antagonists. [3 H]-DHA was used to label CHO-β1 AR for binding studies. The kinetics of ligand binding was assessed using a competition association binding method. Ligand physicochemical properties, including logD7.4 and the immobilized artificial membrane partition coefficient (KIAM ), were assessed using column-based methods. Protein Data Bank (PDB) structures and hydrophobic and electrostatic surface maps were constructed in PyMOL. We demonstrate that the hydrophobic properties of a molecule directly affect its kinetic association rate (kon ) and affinity for the β1 AR. In contrast to our findings at the β2 -adrenoceptor, KIAM , reflecting both hydrophobic and electrostatic interactions of the drug with the charged surface of biological membranes, was no better predictor than simple hydrophobicity measurements such as clogP or logD7.4 , at predicting association rate. Bisoprolol proved kinetically selective for the β1 AR subtype, dissociating 50 times slower and partly explaining its higher measured affinity for the β1 AR. We speculate that the association of positively charged ligands at the β1 AR is curtailed somewhat by its predominantly neutral/positive charged extracellular surface. Consequently, hydrophobic interactions in the ligand-binding pocket dominate the kinetics of ligand binding. In comparison at the β2 AR, a combination of hydrophobicity and negative charge attracts basic, positively charged ligands to the receptor's surface promoting the kinetics of ligand binding. Additionally, we reveal the potential role kinetics plays in the on-target and off-target pharmacology of clinically used β-blockers.
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Affiliation(s)
- David A. Sykes
- Centre of Membrane Proteins and Receptors (COMPARE)University of NottinghamMidlandsUK
- Division of Physiology, Pharmacology & Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Mireia Jiménez‐Rosés
- Centre of Membrane Proteins and Receptors (COMPARE)University of NottinghamMidlandsUK
- Division of Physiology, Pharmacology & Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
| | - John Reilly
- Novartis Institutes for BioMedical ResearchBaselSwitzerland
| | | | - Steven J. Charlton
- Centre of Membrane Proteins and Receptors (COMPARE)University of NottinghamMidlandsUK
- Division of Physiology, Pharmacology & Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Dmitry B. Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE)University of NottinghamMidlandsUK
- Division of Physiology, Pharmacology & Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
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6
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Biswas AD, Catte A, Mancini G, Barone V. Analysis of L-DOPA and droxidopa binding to human β 2-adrenergic receptor. Biophys J 2021; 120:5631-5643. [PMID: 34767786 PMCID: PMC8715240 DOI: 10.1016/j.bpj.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β2-adrenergic receptor (β2AR). The 3.2 Å x-ray crystal structure of human β2AR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors. We show that molecular docking of levodopa (L-DOPA) and droxidopa into rigid and flexible β2AR models leads for both ligands to binding anchor sites comparable to those experimentally reported for adrenaline, namely D113/N312 and S203/S204/S207 side chains. Both ligands have a hydrogen bond network that is extremely similar to those of noradrenaline and dopamine. Interestingly, redocking neutral and protonated versions of adrenaline to rigid and flexible β2AR models results in binding poses that are more energetically stable and distinct from the x-ray crystal structure. Similarly, lowest energy conformations of noradrenaline and dopamine generated by docking into flexible β2AR models had binding free energies lower than those of best poses in rigid receptor models. Furthermore, our findings show that L-DOPA and droxidopa molecules have binding affinities comparable to those predicted for adrenaline, noradrenaline, and dopamine, which are consistent with previous experimental and computational findings and supported by the molecular dynamics simulations of β2AR-ligand complexes performed here.
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7
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Xing G, Woo AYH, Pan L, Lin B, Cheng MS. Recent Advances in β 2-Agonists for Treatment of Chronic Respiratory Diseases and Heart Failure. J Med Chem 2020; 63:15218-15242. [PMID: 33213146 DOI: 10.1021/acs.jmedchem.0c01195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
β2-Adrenoceptor (β2-AR) agonists are widely used as bronchodilators. The emerge of ultralong acting β2-agonists is an important breakthrough in pulmonary medicine. In this review, we will provide mechanistic insights into the application of β2-agonists in asthma, chronic obstructive pulmonary disease (COPD), and heart failure (HF). Recent studies in β-AR signal transduction have revealed opposing functions of the β1-AR and the β2-AR on cardiomyocyte survival. Thus, β2-agonists and β-blockers in combination may represent a novel strategy for HF management. Allosteric modulation and biased agonism at the β2-AR also provide a theoretical basis for developing drugs with novel mechanisms of action and pharmacological profiles. Overlap of COPD and HF presents a substantial clinical challenge but also a unique opportunity for evaluation of the cardiovascular safety of β2-agonists. Further basic and clinical research along these lines can help us develop better drugs and innovative strategies for the management of these difficult-to-treat diseases.
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Affiliation(s)
- Gang Xing
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Anthony Yiu-Ho Woo
- Department of Pharmacology, School of Life Sciences and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Li Pan
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Bin Lin
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mao-Sheng Cheng
- Department of Medicinal Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China.,Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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8
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Plazinska A, Plazinski W. Chirality Effects in Biomolecular Systems: Calculation of the Relative Free Energies by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:5424-5436. [PMID: 32937074 DOI: 10.1021/acs.jcim.0c00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Chirality plays an essential role in chemical and biological sciences. At the molecular level, the effects associated with this phenomenon can be studied by using the well-established technique of molecular dynamics simulations. In this work, we present several approaches suited for the molecular dynamics-based free energy calculation in chiral systems. In particular, we have proposed and tested the following strategies relying on the application of general, enhanced sampling methods: (i) biased sampling in the two-dimensional space, along the coordinates defined by the values of the selected torsional angles; (ii) biased sampling in the one- or two-dimensional space, along the path-based coordinate(s); (iii) rational alteration of the system's Hamiltonian in order to enable the interconversion between stereoisomers and reweighting the biased distribution of configurations; (iv) using the free energy landscape generated within approaches (i) or (ii) as time-independent bias in order to further improve sampling efficiency and simultaneously account for multiple chiral centers. All approaches have been tested on a set of model compounds (fenoterol, fructofuranose, and bromochlorofluoromethane), demonstrating the good performance but also some differences in the range of their applicabilities.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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9
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Babwah AV. The wonderful and masterful G protein-coupled receptor (GPCR): A focus on signaling mechanisms and the neuroendocrine control of fertility. Mol Cell Endocrinol 2020; 515:110886. [PMID: 32574585 DOI: 10.1016/j.mce.2020.110886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/08/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
Abstract
Human GnRH deficiency, both clinically and genetically, is a heterogeneous disorder comprising of congenital GnRH deficiency with anosmia (Kallmann syndrome), or with normal olfaction [normosmic idiopathic hypogonadotropic hypogonadism (IHH)], and adult-onset hypogonadotropic hypogonadism. Our understanding of the neural mechanisms underlying GnRH secretion and GnRH signaling continues to increase at a rapid rate and strikingly, the heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) continue to emerge as essential players in these processes. GPCRs were once viewed as binary on-off switches, where in the "on" state they are bound to their Gα protein, but now we understand that view is overly simplistic and does not adequately characterize GPCRs. Instead, GPCRs have emerged as masterful signaling molecules exploiting different physical conformational states of itself to elicit an array of downstream signaling events via their G proteins and the β-arrestins. The "one receptor-multiple signaling conformations" model is likely an evolved strategy that can be used to our advantage as researchers have shown that targeting specific receptor conformations via biased ligands is proving to be a powerful tool in the effective treatment of human diseases. Can biased ligands be used to selectively modulate signaling by GPCR regulators of the neuroendocrine axis in the treatment of IHH? As discussed in this review, the grand possibility exists. However, while we are still very far from developing these treatments, this exciting likelihood can happen through a much greater mechanistic understanding of how GPCRs signal within the cell.
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Affiliation(s)
- Andy V Babwah
- Department of Pediatrics, Laboratory of Human Growth and Reproductive Development, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States; Child Health Institute of New Jersey, New Brunswick, NJ, United States.
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Ružena Č, Jindra V, Renáta H. Chirality of β2-agonists. An overview of pharmacological activity, stereoselective analysis, and synthesis. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Abstractβ2-Agonists (β2-adrenergic agonists, bronchodilatants, and sympathomimetic drugs) are a group of drugs that are mainly used in asthma and obstructive pulmonary diseases. In practice, the substances used to contain one or more stereogenic centers in their structure and their enantiomers exhibit different pharmacological properties. In terms of bronchodilatory activity, (R)-enantiomers showed higher activity. The investigation of stereoselectivity in action and disposition of chiral drugs together with the preparation of pure enantiomer drugs calls for efficient stereoselective analytical methods. The overview focuses on the stereoselectivity in pharmacodynamics and pharmacokinetics of β2-agonists and summarizes the stereoselective analytical methods for the enantioseparation of racemic beta-agonists (HPLC, LC-MS, GC, TLC, CE). Some methods of the stereoselective synthesis for β2-agonists preparation are also presented.
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Affiliation(s)
- Čižmáriková Ružena
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Valentová Jindra
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Horáková Renáta
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
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Kaproń B, Łuszczki JJ, Płazińska A, Siwek A, Karcz T, Gryboś A, Nowak G, Makuch-Kocka A, Walczak K, Langner E, Szalast K, Marciniak S, Paczkowska M, Cielecka-Piontek J, Ciesla LM, Plech T. Development of the 1,2,4-triazole-based anticonvulsant drug candidates acting on the voltage-gated sodium channels. Insights from in-vivo, in-vitro, and in-silico studies. Eur J Pharm Sci 2018; 129:42-57. [PMID: 30594731 DOI: 10.1016/j.ejps.2018.12.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/26/2018] [Accepted: 12/24/2018] [Indexed: 01/17/2023]
Abstract
The treatment of epilepsy remains difficult mostly since almost 30% of patients suffer from pharmacoresistant forms of the disease. Therefore, there is an urgent need to search for new antiepileptic drug candidates. Previously, it has been shown that 4-alkyl-5-substituted-1,2,4-triazole-3-thione derivativatives possessed strong anticonvulsant activity in a maximal electroshock-induced seizure model of epilepsy. In this work, we examined the effect of the chemical structure of the 1,2,4-triazole-3-thione-based molecules on the anticonvulsant activity and the binding to voltage-gated sodium channels (VGSCs) and GABAA receptors. Docking simulations allowed us to determine the mode of interactions between the investigated compounds and binding cavity of the human VGSC. Selected compounds were also investigated in a panel of ADME-Tox assays, including parallel artificial membrane permeability assay (PAMPA), single cell gel electrophoresis (SCGE) and cytotoxicity evaluation in HepG2 cells. The obtained results indicated that unbranched alkyl chains, from butyl to hexyl, attached to 1,2,4-triazole core are essential both for good anticonvulsant activity and strong interactions with VGSCs. The combined in-vivo, in-vitro and in-silico studies emphasize 4-alkyl-5-substituted-1,2,4-triazole-3-thiones as promising agents in the development of new anticonvulsants.
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Affiliation(s)
- Barbara Kaproń
- Department of Clinical Genetics, Medical University of Lublin, Lublin, Poland
| | | | - Anita Płazińska
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
| | - Agata Siwek
- Department of Pharmacobiology, Jagiellonian University Medical College, Cracow, Poland
| | - Tadeusz Karcz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Cracow, Poland
| | - Anna Gryboś
- Department of Pharmacobiology, Jagiellonian University Medical College, Cracow, Poland
| | - Gabriel Nowak
- Department of Pharmacobiology, Jagiellonian University Medical College, Cracow, Poland
| | - Anna Makuch-Kocka
- Department of Pharmacology, Medical University of Lublin, Lublin, Poland
| | - Katarzyna Walczak
- Department of Pharmacology, Medical University of Lublin, Lublin, Poland
| | - Ewa Langner
- Department of Pharmacology, Medical University of Lublin, Lublin, Poland
| | - Karolina Szalast
- Department of Pharmacology, Medical University of Lublin, Lublin, Poland
| | | | - Magdalena Paczkowska
- Department of Pharmacognosy, Poznan University of Medical Sciences, Poznań, Poland
| | | | - Lukasz M Ciesla
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, USA
| | - Tomasz Plech
- Department of Pharmacology, Medical University of Lublin, Lublin, Poland.
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12
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Studzińska R, Kupczyk D, Płazińska A, Kołodziejska R, Kosmalski T, Modzelewska-Banachiewicz B. Thiazolo[3,2-a]pyrimidin-5-one derivatives as a novel class of 11β-hydroxysteroid dehydrogenase inhibitors. Bioorg Chem 2018; 81:21-26. [PMID: 30086417 DOI: 10.1016/j.bioorg.2018.07.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
11β-hydroxysteroid type 1 dehydrogenase (11β-HSD1) is an enzyme that increases tissue concentrations of cortisol. Selective inhibitors of this enzyme regulate the level of cortisol and thus play a key role in the treatment of Cushing's syndrome, metabolic syndrome and type 2 diabetes. In this study the inhibitory activity of 29 thiazolo[3,2-a]pyrimidin-5-one derivatives on 11β-HSD1 were investigated. Studies were carried out with pooled human liver microsomes. A lot of analyzed compounds show activity for inhibiting 11β-HSD1 (up to 59.15% at concentration 10 µmol/l). Molecular docking simulation show that the molecule of the most active compound: 7-(cyclohexylmethyl)-2-iodomethyl-2,3-dihydrothiazolo[3,2-a]pyrimidin-5-one forms hydrogen bonds with Ala172, Leu171, Leu215 or Tyr177. In addition, the cycloalkane moiety can create the hydrophobic contacts with NADP+. For this compound also the most favourable Docking Score value was obtained. The most active compound only in the slight degree inhibits 11β-HSD2 activity and is a selective inhibitor of 11β-hydroxysteroid dehydrogenase type 1. Consequently it can have a real effect on the regulation of the cortisol level in the body.
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Affiliation(s)
- Renata Studzińska
- Department of Organic Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland.
| | - Daria Kupczyk
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karłowicza 24, 85-092 Bydgoszcz, Poland.
| | - Anita Płazińska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str. 4a, 20-093 Lublin, Poland.
| | - Renata Kołodziejska
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karłowicza 24, 85-092 Bydgoszcz, Poland.
| | - Tomasz Kosmalski
- Department of Organic Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland.
| | - Bożena Modzelewska-Banachiewicz
- Department of Organic Chemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Jurasza 2, 85-089 Bydgoszcz, Poland.
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13
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Plazinska A, Plazinski W, Luchowski R, Wnorowski A, Grudzinski W, Gruszecki WI. Ligand-induced action of the W286 6.48 rotamer toggle switch in the β 2-adrenergic receptor. Phys Chem Chem Phys 2017; 20:581-594. [PMID: 29226293 DOI: 10.1039/c7cp04808d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies focused on GPCRs, particularly on the β2-adrenergic receptor (β2-AR), have demonstrated the relationship between ligand structure, receptor conformational changes and the corresponding pharmacological outcomes. Herein, we studied the molecular details of the rotameric flip of the W2866.48 sidechain, i.e. a presumed action switch that has not been reported in native β2-AR thus far. It is believed that although both the 'active' and 'inactive' conformers of β2-AR exhibit similar conformations of this switch, it may still play a substantial role in the ligand-induced activation of the receptor. By using both experimental methods (time-resolved fluorescence spectroscopy) and molecular modeling techniques (enhanced-sampling molecular dynamics), we characterized the conformational rearrangements of W2866.48 in relation to the type of ligand present in the binding cavity and to the conformation of the receptor ('active' vs. 'inactive' β2-AR). We found that the conformational behaviour of W2866.48 is correlated with the pharmacological character of the ligand present in the binding cavity but not with the instantaneous conformation of the receptor. Namely, agonists promote the W2866.48 conformations that facilitate the increase of the solvation within the inner receptor channel. In contrast, antagonists and inverse agonists act toward the decrease of the solvation in the inner channel. This creates an opportunity for using computational methodologies in determining the pharmacological properties of various ligands. The combination of the time-resolved fluorescence spectroscopy technique with the enhanced-sampling molecular dynamics simulations is shown to be a powerful tool for studying the ligand-induced conformational rearrangements in GPCRs.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093 Lublin, Poland.
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14
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Cameron RB, Peterson YK, Beeson CC, Schnellmann RG. Structural and pharmacological basis for the induction of mitochondrial biogenesis by formoterol but not clenbuterol. Sci Rep 2017; 7:10578. [PMID: 28874749 PMCID: PMC5585315 DOI: 10.1038/s41598-017-11030-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial dysfunction is associated with numerous acute and chronic degenerative diseases. The beta-2 adrenergic receptor (β2AR) agonist formoterol induces mitochondrial biogenesis (MB), but other β2AR agonists, such as clenbuterol, do not. We sought to identify the MB signaling pathway of formoterol and the differences in signaling between these two ligands that result in the differential induction of MB. While formoterol and clenbuterol increased cAMP, only formoterol increased the phosphorylation of Akt and its downstream target eNOS. The increase in Akt phosphorylation was Gβγ- and PI3K-dependent, and the increase in eNOS phosphorylation was Gβγ- and Akt-dependent. Only formoterol increased cGMP. Formoterol induced MB as measured by increases in uncoupled cellular respiration and PGC-1α and NDUFS1 mRNA expression and was blocked by inhibitors of Gβγ, Akt, NOS, and soluble guanylate cyclase. To identify distinct receptor-ligand interactions leading to these differences in signaling, we docked formoterol and clenbuterol to six structures of the β2AR. Compared to clenbuterol, the methoxyphenyl group of formoterol interacted more frequently with V114 and F193, while its formamide group interacted more frequently with C191. These data indicate that the unique structural features of formoterol allow it to interact with the β2AR to activate the Gβγ-Akt-eNOS-sGC pathway to induce MB.
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Affiliation(s)
- Robert B Cameron
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.,Department of Drug Discovery and Biomedical Sciences, College of Graduate Studies, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Yuri K Peterson
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, MSC139, 70 President St., Charleston, SC, 29425-8906, USA
| | - Craig C Beeson
- Department of Drug Discovery and Biomedical Sciences, College of Graduate Studies, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Rick G Schnellmann
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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15
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Flieger J, Feder-Kubis J, Tatarczak-Michalewska M, Płazińska A, Madejska A, Swatko-Ossor M. Natural terpene derivatives as new structural task-specific ionic liquids to enhance the enantiorecognition of acidic enantiomers on teicoplanin-based stationary phase by high-performance liquid chromatography. J Sep Sci 2017; 40:2374-2381. [PMID: 28426156 DOI: 10.1002/jssc.201700197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/31/2017] [Accepted: 04/01/2017] [Indexed: 11/06/2022]
Abstract
We present the specific cooperative effect of a semisynthetic glycopeptide antibiotic teicoplanin and chiral ionic liquids containing the (1R,2S,5R)-(-)-menthol moiety on the chiral recognition of enantiomers of mandelic acid, vanilmandelic acid, and phenyllactic acid. Experiments were performed chromatographically on an Astec Chirobiotic T chiral stationary phase applying the mobile phase with the addition of the chiral ionic liquids. The stereoselective binding of enantiomers to teicoplanin in presence of new chiral ionic liquids were evaluated applying thermodynamic measurements and the docking simulations. Both the experimental and theoretical methods revealed that the chiral recognition of enantiomers in the presence of new chiral ionic liquids was enthalpy driven. The changes of the teicoplanin conformation occurring upon binding of the chiral ionic liquids are responsible for the differences in the standard changes in Gibbs energy (ΔG0 ) values obtained for complexes formed by the R and S enantiomers and teicoplanin. Docking simulations revealed the steric adjustment between the chiral ionic liquids cyclohexane ring (chair conformation) and the β-d-glucosamine ring of teicoplanin and additionally hydrophobic interactions between the decanoic aliphatic chain of teicoplanin and the alkyl group of the tested salts. The obtained terpene derivatives can be considered as "structural task-specific ionic liquids" responsible for enhancing the chiral resolution in synergistic systems with two chiral selectors.
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Affiliation(s)
- Jolanta Flieger
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
| | - Joanna Feder-Kubis
- Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | | | - Anita Płazińska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Anna Madejska
- Department of Analytical Chemistry, Medical University of Lublin, Lublin, Poland
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology, Medical University of Lublin, Lublin, Poland
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16
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Plazinska A, Plazinski W. Stereoselective binding of agonists to the β2-adrenergic receptor: insights into molecular details and thermodynamics from molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2017; 13:910-920. [DOI: 10.1039/c6mb00814c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enhanced-sampling molecular dynamics simulations show the molecular details of stereospecific binding of agonists to the β2-adrenergic receptor.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy
- Faculty of Pharmacy
- Medical University of Lublin
- 20-093 Lublin
- Poland
| | - Wojciech Plazinski
- J. Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- 30-239 Cracow
- Poland
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17
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Feder-Kubis J, Flieger J, Tatarczak-Michalewska M, Płazińska A, Madejska A, Swatko-Ossor M. Renewable sources from plants as the starting material for designing new terpene chiral ionic liquids used for the chromatographic separation of acidic enantiomers. RSC Adv 2017. [DOI: 10.1039/c7ra03310a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesis of cheap and natural resources is an important topic in green chemistry.
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Affiliation(s)
- Joanna Feder-Kubis
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Jolanta Flieger
- Department of Analytical Chemistry
- Medical University of Lublin
- 20-093 Lublin
- Poland
| | | | - Anita Płazińska
- Department of Biopharmacy
- Medical University of Lublin
- 093 Lublin
- Poland
| | - Anna Madejska
- Department of Analytical Chemistry
- Medical University of Lublin
- 20-093 Lublin
- Poland
| | - Marta Swatko-Ossor
- Department of Biochemistry and Biotechnology
- Medical University of Lublin
- 20-093 Lublin
- Poland
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18
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Yang Z, Lu ZQ, Zhang YJ, Li YB, Wang ZY, Zhang YL, Zhuang PW, Bai G. Looking for agonists of β2 adrenergic receptor from Fuzi and Chuanwu by virtual screening and dual-luciferase reporter assay. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2016; 18:550-561. [PMID: 26700061 DOI: 10.1080/10286020.2015.1123692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
More and more studies demonstrated that β2 adrenergic receptor (β2-AR) plays a crucial role for the treatment of heart failure. Chuanwu and Fuzi have been used over thousands of years in China for the treatment of heart failure. Considering the effects of these herbs are very similar to β2-AR agonists, we presume whether β2-AR agonists can be found from Fuzi and Chuanwu. Fuzi and Chuanwu decoction were used to receive the luciferase reporter activity assay to verify the hypothesis, and the result is positive and encouraging. For it is very difficult to get all of the monomer compounds of Fuzi and Chuanwu, virtual screening was used to find potential β2-AR agonists and a cell-based β2-AR agonist functional evaluation model, combined with a luciferase reporter assay system, was used to confirm the final result. In this research, 45 compounds were identified as β2-AR agonists, and four compounds were verified and the rest need further experiment.
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Affiliation(s)
- Zhen Yang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Zhi-Qiang Lu
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Yan-Jun Zhang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Yu-Bo Li
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Zeng-Yong Wang
- b State Key Laboratory of Medicinal Chemical Biology , Nankai University , Tianjin 300071 , China
| | - Yan-Ling Zhang
- c School of Chinese Pharmacy , Beijing University of Traditional Chinese Medicine , Beijing 100102 , China
| | - Peng-Wei Zhuang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
- d Tianjin JF-Pharmaland Technology Development Co., Ltd. , Tianjin 300457 , China
| | - Gang Bai
- b State Key Laboratory of Medicinal Chemical Biology , Nankai University , Tianjin 300071 , China
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19
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Gaye MM, Nagy G, Clemmer DE, Pohl NLB. Multidimensional Analysis of 16 Glucose Isomers by Ion Mobility Spectrometry. Anal Chem 2016; 88:2335-44. [PMID: 26799269 DOI: 10.1021/acs.analchem.5b04280] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diastereomeric adducts comprising an enantiomerically pure monosaccharide analyte, a peptide, and/or an amino acid and a divalent metal ion (for 16 different monosaccharide isomers) are generated by electrospray ionization and analyzed by combined ion mobility spectrometry-mass spectrometry (IMS-MS) techniques. Mobility distributions of [l-Ser + M + H](+) (where l-Ser is l-serine and M is a given monosaccharide), [l-Phe-Gly + M + H](+) (where l-Phe-Gly is l-phenylalanine-glycine), and [Mn(II) + (l-Phe-Gly - H) + M](+) complex ions are used to determine collision cross sections (ccs in Å(2)), and groups of cross sections for different clusters are proposed as means of identifying the sugar isomers. Within one type of complex, variations in ccs do not always allow delineation between the 16 glucose isomers, but interestingly, when ccs of three different ions are combined as a spatial vector, enantiomers are partially resolved. As a result of this analysis, l-glucose, d-glucose, l-allose, d-allose, d-gulose, d-galactose, and l-mannose are delineated, and for all eight enantiomeric pairs, d and l entities display different coordinates. In addition, different combinations of amino acids, peptide, and metal ions are surveyed, and the potential for yielding unique coordinates for the generated diastereomeric complexes is assessed.
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Affiliation(s)
- M M Gaye
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - G Nagy
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - D E Clemmer
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - N L B Pohl
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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20
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Towards predictive docking at aminergic G-protein coupled receptors. J Mol Model 2015; 21:284. [PMID: 26453085 DOI: 10.1007/s00894-015-2824-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/15/2015] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) are hard to crystallize. However, attempts to predict their structure have boomed as a result of advancements in crystallographic techniques. This trend has allowed computer-aided molecular modeling of GPCRs. We analyzed the performance of four molecular modeling programs in pose evaluation of re-docked antagonists / inverse agonists to 11 original crystal structures of aminergic GPCRs using an induced fit-docking procedure. AutoDock and Glide were used for docking. AutoDock binding energy function, GlideXP, Prime MM-GB/SA, and YASARA binding function were used for pose scoring. Root mean square deviation (RMSD) of the best pose ranged from 0.09 to 1.58 Å, and median RMSD of the top 60 poses ranged from 1.47 to 3.83 Å. However, RMSD of the top pose ranged from 0.13 to 7.33 Å and ranking of the best pose ranged from the 1st to 60th out of 60 poses. Moreover, analysis of ligand-receptor interactions of top poses revealed substantial differences from interactions found in crystallographic structures. Bad ranking of top poses and discrepancies between top docked poses and crystal structures render current simple docking methods unsuitable for predictive modeling of receptor-ligand interactions. Prime MM-GB/SA optimized for 3NY9 by multiple linear regression did not work well at 3NY8 and 3NYA, structures of the same receptor with different ligands. However, 9 of 11 trajectories of molecular dynamics simulations by Desmond of top poses converged with trajectories of crystal structures. Key interactions were properly detected for all structures. This procedure also worked well for cross-docking of tested β2-adrenergic antagonists. Thus, this procedure represents a possible way to predict interactions of antagonists with aminergic GPCRs.
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21
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Plazinska A, Plazinski W, Jozwiak K. Agonist binding by the β2-adrenergic receptor: an effect of receptor conformation on ligand association-dissociation characteristics. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:149-63. [PMID: 25726162 PMCID: PMC4359354 DOI: 10.1007/s00249-015-1010-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/20/2014] [Accepted: 01/31/2015] [Indexed: 01/01/2023]
Abstract
The β2-adrenergic receptor (β2-AR), a G protein-coupled receptor (GPCR), is a physiologically important transmembrane protein that is a target for drugs used for treatment of asthma and cardiovascular diseases. Study of the first steps of ligand recognition and the molecular basis of ligand binding to the orthosteric site is essential for understanding the pharmacological properties of the receptor. In this work we investigated the characteristic features of the agonist association–dissociation process to and from the different conformational forms of β2-AR by use of advanced molecular modeling techniques. The investigation was focused on estimating the free energy profiles (FEPs) corresponding to the process of a full agonist ((R,R)-fenoterol) and an inverse agonist (carazolol) binding and unbinding to and from β2-AR. The two different conformational forms of β2-AR, i.e. active β2-AR–PDB: 3P0G and inactive β2-AR–PDB: 2RH1 were included in this stage of the study. We revealed several significant qualitative differences between FEPs characteristic of both conformational forms. Both FEPs suggest the existence of three transient binding sites in the extracellular domain of β2-AR. Comparison of the residues surrounding these transient binding sites in both β2-AR states revealed the importance of the aromatic residues F194, H932.64, H2966.58, and H178 (extracellular part of β2-AR) in the early stages of the binding process. In addition, slightly different exit and entry paths are preferred by the ligand molecule in the extracellular part of β2-AR, depending on the conformation of the receptor.
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Affiliation(s)
- Anita Plazinska
- Laboratory of Medicinal Chemistry and Neuroengineering, Department of Chemistry, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093, Lublin, Poland
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22
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Woo AYH, Song Y, Zhu W, Xiao RP. Advances in receptor conformation research: the quest for functionally selective conformations focusing on the β2-adrenoceptor. Br J Pharmacol 2015; 172:5477-88. [PMID: 25537131 DOI: 10.1111/bph.13049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/14/2014] [Indexed: 01/14/2023] Open
Abstract
Seven-transmembrane receptors, also called GPCRs, represent the largest class of drug targets. Upon ligand binding, a GPCR undergoes conformational rearrangement and thereby changes its interaction with effector proteins including the cognate G-proteins and the multifunctional adaptor proteins, β-arrestins. These proteins, by initiating distinct signal transduction mechanisms, mediate one or several functional responses. Recently, the concept of ligand-directed GPCR signalling, also called functional selectivity or biased agonism, has been proposed to explain the phenomenon that chemically diverse ligands exhibit different efficacies towards the different signalling pathways of a single GPCR, and thereby act as functionally selective or 'biased' ligands. Current concepts support the notion that ligand-specific GPCR conformations are the basis of ligand-directed signalling. Multiple studies using fluorescence spectroscopy, X-ray crystallography, mass spectroscopy, nuclear magnetic resonance spectroscopy, single-molecule force spectroscopy and other techniques have provided the evidence to support this notion. It is anticipated that these techniques will ultimately help elucidate the structural basis of ligand-directed GPCR signalling at a precision meaningful for structure-based drug design and how a specific ligand molecular structure induces a unique receptor conformation leading to biased signalling. In this review, we will summarize recent advances in experimental techniques applied in the study of functionally selective GPCR conformations and breakthrough data obtained in these studies particularly those of the β2-adrenoceptor.
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Affiliation(s)
- Anthony Yiu-Ho Woo
- Institute of Molecular Medicine, Centre for Life Sciences, Peking University, Beijing, China.,Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ying Song
- Institute of Molecular Medicine, Centre for Life Sciences, Peking University, Beijing, China
| | - Weizhong Zhu
- Department of Pharmacology, Nantong University School of Pharmacy, Nantong, China
| | - Rui-Ping Xiao
- Institute of Molecular Medicine, Centre for Life Sciences, Peking University, Beijing, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
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23
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Interaction of fenoterol stereoisomers with β2-adrenoceptor-G sα fusion proteins: antagonist and agonist competition binding. Naunyn Schmiedebergs Arch Pharmacol 2015; 388:517-24. [PMID: 25637582 DOI: 10.1007/s00210-015-1086-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/09/2015] [Indexed: 10/24/2022]
Abstract
The specific interaction between G-protein-coupled receptors and ligand is the starting point for downstream signaling. Fenoterol stereoisomers were successfully used to probe ligand-specific activation (functional selectivity) of the β2-adrenoceptor (β2AR) (Reinartz et al. 2015). In the present study, we extended the pharmacological profile of fenoterol stereoisomers using β2AR-Gsα fusion proteins in agonist and antagonist competition binding assays. Dissociations between binding affinities and effector potencies were found for (R,S')- and (S,S')-isomers of 4'-methoxy-1-naphthyl-fenoterol. Our data corroborate former studies on the importance of the aminoalkyl moiety of fenoterol derivatives for functional selectivity.
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24
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Reprint of: fRMSDchiral: a novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 968:26-31. [PMID: 24929899 DOI: 10.1016/j.jchromb.2014.05.012] [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: 11/29/2013] [Revised: 02/10/2014] [Accepted: 02/19/2014] [Indexed: 11/20/2022]
Abstract
The ability of molecules to distinguish between optical isomers is crucial for living systems. The change of position of one enantiomer in respect to the position of the second enantiomer within an asymmetric binding site may be analyzed on different levels. Root Mean Square Deviation (RMSD) may be used for such analyses with low precision. Additional fragment level variants of RMSD allow for more precise definition of differences in location of the main molecular features responsible for recognition of stereoisomers by a selector. Three fRMSDchiral parameters appear to be very useful to precisely quantify the change in orientations of stereoisomers. Proposed calculation emerges as interesting assistance in interpretation of consequences of formation differential interaction(s) responsible for a chiral recognition process.
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25
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Woo AYH, Jozwiak K, Toll L, Tanga MJ, Kozocas JA, Jimenez L, Huang Y, Song Y, Plazinska A, Pajak K, Paul RK, Bernier M, Wainer IW, Xiao RP. Tyrosine 308 is necessary for ligand-directed Gs protein-biased signaling of β2-adrenoceptor. J Biol Chem 2014; 289:19351-63. [PMID: 24831005 DOI: 10.1074/jbc.m114.558882] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Interaction of a given G protein-coupled receptor to multiple different G proteins is a widespread phenomenon. For instance, β2-adrenoceptor (β2-AR) couples dually to Gs and Gi proteins. Previous studies have shown that cAMP-dependent protein kinase (PKA)-mediated phosphorylation of β2-AR causes a switch in receptor coupling from Gs to Gi. More recent studies have demonstrated that phosphorylation of β2-AR by G protein-coupled receptor kinases, particularly GRK2, markedly enhances the Gi coupling. We have previously shown that although most β2-AR agonists cause both Gs and Gi activation, (R,R')-fenoterol preferentially activates β2-AR-Gs signaling. However, the structural basis for this functional selectivity remains elusive. Here, using docking simulation and site-directed mutagenesis, we defined Tyr-308 as the key amino acid residue on β2-AR essential for Gs-biased signaling. Following stimulation with a β2-AR-Gs-biased agonist (R,R')-4'-aminofenoterol, the Gi disruptor pertussis toxin produced no effects on the receptor-mediated ERK phosphorylation in HEK293 cells nor on the contractile response in cardiomyocytes expressing the wild-type β2-AR. Interestingly, Y308F substitution on β2-AR enabled (R,R')-4'-aminofenoterol to activate Gi and to produce these responses in a pertussis toxin-sensitive manner without altering β2-AR phosphorylation by PKA or G protein-coupled receptor kinases. These results indicate that, in addition to the phosphorylation status, the intrinsic structural feature of β2-AR plays a crucial role in the receptor coupling selectivity to G proteins. We conclude that specific interactions between the ligand and the Tyr-308 residue of β2-AR stabilize receptor conformations favoring the receptor-Gs protein coupling and subsequently result in Gs-biased agonism.
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Affiliation(s)
- Anthony Yiu-Ho Woo
- From the Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China, the Institute of Molecular Medicine, Centers for Life Sciences, Peking University, Beijing 100871, China, the Laboratory of Cardiovascular Science and
| | - Krzysztof Jozwiak
- the Department of Chemistry, Medical University of Lublin, Lublin, Poland
| | - Lawrence Toll
- the Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, and
| | | | | | | | - Ying Huang
- From the Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China, the Institute of Molecular Medicine, Centers for Life Sciences, Peking University, Beijing 100871, China
| | - Ying Song
- From the Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China, the Institute of Molecular Medicine, Centers for Life Sciences, Peking University, Beijing 100871, China
| | - Anita Plazinska
- the Department of Chemistry, Medical University of Lublin, Lublin, Poland
| | - Karolina Pajak
- the Department of Chemistry, Medical University of Lublin, Lublin, Poland
| | - Rajib K Paul
- Laboratory of Clinical Investigation, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Michel Bernier
- Laboratory of Clinical Investigation, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Irving W Wainer
- Laboratory of Clinical Investigation, NIA, National Institutes of Health, Baltimore, Maryland 21224
| | - Rui-Ping Xiao
- the Institute of Molecular Medicine, Centers for Life Sciences, Peking University, Beijing 100871, China,
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26
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fRMSDchiral: a novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 955-956:110-5. [PMID: 24631819 DOI: 10.1016/j.jchromb.2014.02.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/10/2014] [Accepted: 02/19/2014] [Indexed: 11/21/2022]
Abstract
The ability of molecules to distinguish between optical isomers is crucial for living systems. The change of position of one enantiomer in respect to the position of the second enantiomer within an asymmetric binding site may be analyzed on different levels. Root Mean Square Deviation (RMSD) may be used for such analyses with low precision. Additional fragment level variants of RMSD allow for more precise definition of differences in location of the main molecular features responsible for recognition of stereoisomers by a selector. Three fRMSDchiral parameters appear to be very useful to precisely quantify the change in orientations of stereoisomers. Proposed calculation emerges as interesting assistance in interpretation of consequences of formation differential interaction(s) responsible for a chiral recognition process.
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27
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Plazinska A, Plazinski W, Jozwiak K. Fast, metadynamics-based method for prediction of the stereochemistry-dependent relative free energies of ligand-receptor interactions. J Comput Chem 2014; 35:876-82. [PMID: 24615679 DOI: 10.1002/jcc.23563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 01/09/2023]
Abstract
The computational approach applicable for the molecular dynamics (MD)-based techniques is proposed to predict the ligand-protein binding affinities dependent on the ligand stereochemistry. All possible stereoconfigurations are expressed in terms of one set of force-field parameters [stereoconfiguration-independent potential (SIP)], which allows for calculating all relative free energies by only single simulation. SIP can be used for studying diverse, stereoconfiguration-dependent phenomena by means of various computational techniques of enhanced sampling. The method has been successfully tested on the β2-adrenergic receptor (β2-AR) binding the four fenoterol stereoisomers by both metadynamics simulations and replica-exchange MD. Both the methods gave very similar results, fully confirming the presence of stereoselective effects in the fenoterol-β2-AR interactions. However, the metadynamics-based approach offered much better efficiency of sampling which allows for significant reduction of the unphysical region in SIP.
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Affiliation(s)
- Anita Plazinska
- Department of Chemistry, Faculty of Pharmacy, Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, W. Chodzki Street, 4a, 20-093, Lublin, Poland
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