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Tarenzi T, Calandrini V, Potestio R, Carloni P. Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes. J Chem Theory Comput 2019; 15:2101-2109. [PMID: 30763087 PMCID: PMC6433333 DOI: 10.1021/acs.jctc.9b00040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
G-protein-coupled receptors (GPCRs) constitute as much as 30% of the overall proteins targeted by FDA-approved drugs. However, paucity of structural experimental information and low sequence identity between members of the family impair the reliability of traditional docking approaches and atomistic molecular dynamics simulations for in silico pharmacological applications. We present here a dual-resolution approach tailored for such low-resolution models. It couples a hybrid molecular mechanics/coarse-grained (MM/CG) scheme, previously developed by us for GPCR-ligand complexes, with a Hamiltonian-based adaptive resolution scheme (H-AdResS) for the solvent. This dual-resolution approach removes potentially inaccurate atomistic details from the model while building a rigorous statistical ensemble-the grand canonical one-in the high-resolution region. We validate the method on a well-studied GPCR-ligand complex, for which the 3D structure is known, against atomistic simulations. This implementation paves the way for future accurate in silico studies of low-resolution ligand/GPCRs models.
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Affiliation(s)
- Thomas Tarenzi
- Computation-based Science and Technology Research Center CaSToRC , The Cyprus Institute , 20 Konstaninou Kavafi Street , 2121 Aglantzia, Nicosia , Cyprus
- Departments of Physics , Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal Straße , 52062 Aachen , Germany
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Vania Calandrini
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Raffaello Potestio
- Department of Physics , University of Trento , via Sommarive 14 Povo , Trento 38123 , Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications , I-38123 Trento , Italy
| | - Paolo Carloni
- Departments of Physics , Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal Straße , 52062 Aachen , Germany
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
- JARA-HPC, Jülich Supercomputing Center , Forschungszentrum Jülich , 52428 Jülich , Germany
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Ahmed M, Ishiguro M, Nagatomo T. Molecular modeling of SWR-0342SA, a β3-selective agonist, with β1- and β3-adrenoceptor. Life Sci 2006; 78:2019-23. [PMID: 16310810 DOI: 10.1016/j.lfs.2005.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Accepted: 09/13/2005] [Indexed: 10/25/2022]
Abstract
The molecular dynamics (MD) simulations study in the formation of the complex between compound SWR-0342SA and beta-ARs suggested that upon binding SWR-0342SA stimulates receptor activation through residues network (Asp104, Leu335 in beta(1)-AR; Asp117, Ser209, Leu303, Ser191 in beta(3)-AR) in an active conformation state. The models suggest that the structural origin of the selectivity of SWR-0342SA to beta(3)-AR vs. beta(1)-AR comes from the following results: (a) the tight interaction between the agonist and the TMs 3, 5, 6 and 2 nd EC loop. Asp117 interacts with the cationic amino group of the agonist molecule. (b) Additional contacts are done with Ser209, Leu303 and Ser191. These results are in good agreement with the binding affinities (pKi values) of SWR-0342SA to beta-AR family expressed in recombinant mammalian cells.
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Affiliation(s)
- Maruf Ahmed
- Department of Pharmacology, Niigata University of Pharmacy and Applied Life Sciences, Niigata 950-2081, Japan
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Nandakumar K, Bansal SK, Singh R, Mohite AJ, Bodhankar SL, Jindal DP, Coumar MS, Balaraman R, Bhardwaj SH. Study of β-Adrenoreceptor Antagonistic Activity of DPJ 904 in Rats. Pharmacology 2005; 74:1-5. [PMID: 15627847 DOI: 10.1159/000082861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 10/15/2004] [Indexed: 11/19/2022]
Abstract
beta-Adrenoreceptor antagonistic activity of a newly synthesized compound was evaluated in vivo by measuring the mean arterial blood pressure and heart rate of urethane-anesthetized rats treated with isoprenaline. In vitro beta(1)-, beta(2)- and beta(3)-antagonism was studied using isolated rat right atria, isolated rat uterus and isolated rat colon preparations, respectively, in comparison to isoprenaline response. DPJ 904 (1, 3 and 10 mg/kg, i.v.) produced dose-dependent hypotensive and bradycardia response in anesthetized rat. DPJ 904 (1, 3 and 10 mg/kg, i.v.) significantly inhibited both the tachycardial effects and hypotensive response induced by isoprenaline. DPJ 904-antagonized isoprenaline induced positive chronotropic effects of isolated rat right atria and a uterine relaxant effect indicating beta(1)- and beta(2)-blockade. The parallel shift to the right of the concentration-response curve of isoprenaline in the presence of DPJ 904 in KCl (30 mmol/l) induced contraction of the rat colon suggesting that DPJ 904 also possessed beta(3)-adrenoreceptor antagonistic activity. The selectivity to beta(1)-adrenoreceptor was nearly 20.5 times greater than to beta(2)-adrenoreceptor. The present study indicates that DPJ 904 possesses beta-adrenoreceptor antagonistic activity with slightly more affinity to the beta(1)-adrenoreceptor subtype.
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Affiliation(s)
- K Nandakumar
- Department of Pharmacology, Poona College of Pharmacy, Bharati Vidyapeeth Deemed University, Erandwane, Pune, India
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Nagatomo T, Ohnuki T, Ishiguro M, Ahmed M, Nakamura T. Beta-adrenoceptors: three-dimensional structures and binding sites for ligands. JAPANESE JOURNAL OF PHARMACOLOGY 2001; 87:7-13. [PMID: 11676201 DOI: 10.1254/jjp.87.7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recent progress in analyzing the structures and functions of G-protein coupled receptors (GPCRs) including beta-adrenoceptors (beta-ARs) has been made by pharmacological, physiological and molecular biological techniques. The three-dimensional (3D) structures, interaction sites with ligands and conformational changes of these receptor subtypes due to ligand binding are now better understood by the simulation of these receptors using computer-aided molecular modeling. Based on these techniques, numbers and conformations of amino acid sequences of each subtype (beta1-, beta2- and beta3-ARs) were defined and also interaction sites or modes of interaction between ligands and beta-ARs could be analyzed three-dimensionally. In addition, simulation of 3D structures of beta-ARs by molecular modeling could clearly determine the limited size, space or pocket for fitting with ligands. These studies will give some clues for the clarification of other GPCRs. Thus, this review summarizes current findings on chemical structures of ligands, amino acid sequences, 3D structures and important amino acids of beta-AR subtypes for interacting with ligands obtained from mutagenesis, chimeric studies and molecular modeling techniques.
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Affiliation(s)
- T Nagatomo
- Department of Pharmacology, Niigata College of Pharmacy, Japan.
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Hwang SK, Juhasz A, Yoon SH, Bodor N. Soft drugs. 12. Design, synthesis, and evaluation of soft bufuralol analogues. J Med Chem 2000; 43:1525-32. [PMID: 10780909 DOI: 10.1021/jm9904654] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for more potent but still short-acting beta-blockers (BB), the methyl, ethyl, isopropyl, tert-butyl, cyclohexyl, 2-(1-adamantyl)ethyl, and methylthiomethyl esters of the acidic inactive metabolite of bufuralol were synthesized based on the "inactive metabolite" approach. The cleavage of the ester bond by blood and tissue esterases rapidly deactivates these compounds, resulting in an ultrashort duration of action. The beta-antagonist potencies and time courses of actions of the new "soft" BBs were characterized by recording ECG and intra-arterial blood pressure (BP) in rats. In the isoproterenol-induced tachycardia model, while bufuralol at an iv dose of 1 mg/kg (3.8 micromol/kg) diminished heart rate (HR) for at least 2 h, the effects of the soft drugs lasted for only 10-30 min at equimolar dose. The inactive metabolite did not decrease HR significantly. The first four members of this series of compounds showed the highest beta-blocking potencies, ranging between 25% and 50% of that of bufuralol. Next, the effects of these most active compounds on resting HR and BP were evaluated in comparison to esmolol. Infused for 10 min at a rate of 20 micromol/kg/min, esmolol decreased HR and mean arterial pressure (MAP) by 40% and 60%, respectively. The soft drugs at doses ranging only between 2 and 4 micromol/kg/min resulted in a 20-40% decrease in HR and a 30-50% reduction in MAP. However, the time courses of both the bradycardic and hypotensive effects of the soft drugs were superimposable to that of esmolol, diminishing within 60 min after the discontinuation of the infusions.
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Affiliation(s)
- S K Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 442-749, Korea
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Chen YL, Wang TC, Lee KH, Tzeng CC, Chang YL, Teng CM. Synthesis of Coumarin Derivatives as Inhibitors of Platelet Aggregation. Helv Chim Acta 1996. [DOI: 10.1002/hlca.19960790308] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Méjean A, Guillaume JL, Strosberg AD. Carazolol: a potent, selective beta 3-adrenoceptor agonist. Eur J Pharmacol 1995; 291:359-66. [PMID: 8719421 DOI: 10.1016/0922-4106(95)90077-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Carazolol is a beta1/beta2 adrenoceptor antagonist of high potency used in the treatment of hypertension. Its affinity for the beta 3-adrenoceptor was determined in Chinese hamster ovary cells transfected with the gene of the human or the murine beta 3-adrenoceptor. Carazolol is recognized with a nanomolar affinity, which positions it among the best ligands for beta 3-adrenoceptors. The adenylyl cyclase stimulation was measured in transfected cells where carazolol acted as a full agonist on both murine and human receptor subtypes. Furthermore, in murine adipocyte-like 3T3-F442A cells, which express beta 3-adrenoceptor naturally, carazolol induced lipolysis. This compound also appeared to be a useful tool for molecular characterization of the beta 3-adrenoceptor, unlike the classical beta 3-adrenoceptor agonists, carazolol conferred an appreciable protection of receptor binding sites against inactivation by the reducing agent dithiothreitol. The major iodinated analog of carazolol retained its binding characteristics for the beta 3-adrenoceptor and remained an efficient adenylyl cyclase stimulator in cells expressing human beta 3-adrenoceptor.
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Affiliation(s)
- A Méjean
- Institut Cochin de Génétique Moléculaire, Laboratoire d' Immuno-Pharmacologie Moléculaire, CNRS-UPR 0415, Paris, France
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Fantucci P, Mattioli E, Villa AM, Villa L. Conformational behaviour and molecular similarity of some beta 1-adrenergic ligands. J Comput Aided Mol Des 1992; 6:315-30. [PMID: 1328545 DOI: 10.1007/bf00125942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The conformational behaviour of a series of aryloxypropanolamines was investigated by means of a new procedure which allows the sampling of the molecular torsional surface in a very efficient way. The combination of such a procedure with the standard molecular mechanics algorithms for the geometry optimization gives, as a result, the definition of a powerful computational scheme for the detailed analysis of the potential energy surface of complex molecules. The compounds studied show a remarkable tendency to form intra-molecular hydrogen bonds, which seem to play a key role in determining the lowest energy structures. The indices of molecular similarity proposed by Carbó, computed for the most stable conformers, do not account for differences between diastereoisomers, and, as a consequence, can hardly be used to attempt a structure-activity correlation.
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Affiliation(s)
- P Fantucci
- Dipartimento di Chimica Inorganica, Milan, Italy
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Cecchetti V, Schiaffella F, Tabarrini O, Zhou W, Fravolini A, Goi A, Bruni G, Segre G. Symbiotic approach to drug design: N-[(4-chloro-3-sulfamoylbenzamido)-ethyl]propanolamine derivatives as β-adrenergic blocking agents with diuretic activity. Eur J Med Chem 1991. [DOI: 10.1016/0223-5234(91)90098-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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el Tayar N, Testa B, van de Waterbeemd H, Carrupt PA, Kaumann AJ. Influence of lipophilicity and chirality on the selectivity of ligands for beta 1- and beta 2-adrenoceptors. J Pharm Pharmacol 1988; 40:609-12. [PMID: 2907026 DOI: 10.1111/j.2042-7158.1988.tb05319.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Eudismic and QSAR analyses are reported for the beta 1- and beta 2-adrenoceptor affinities and beta 1-selectivity of 10 enantiomeric pairs of ligands with only N-isopropyl or N-t-butyl groups. For both receptors, the eudismic index (ratio of affinity) increases with the affinity of the eutomers. However, the affinity of the distomers for the beta 2-adrenoceptor is relatively high, suggesting additional hydrophobic interactions. This is confirmed by various correlations between affinities and lipophilicities, showing that the affinity for beta 2-adrenoceptors is slightly more dependent on lipophilicity than that for beta 1-adrenoceptors. As a result, the beta 1-selectivity of the investigated beta 1-adrenoceptor ligands is strongly and negatively correlated with their lipophilicity (r = -0.942).
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Affiliation(s)
- N el Tayar
- School of Pharmacy, University of Lausanne, Switzerland
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