1
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Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-1-4939-7404-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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2
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Yoneyama H, Yamamoto D, Yamatodani A, Harusawa S. Efficient Approaches to <i>S</i>-alkyl-<i>N</i>-alkylisothioureas and Application to Novel Histamine H<sub>3</sub>R Antagonists. YAKUGAKU ZASSHI 2016; 136:1217-32. [DOI: 10.1248/yakushi.16-00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hiroki Yoneyama
- Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences
| | | | | | - Shinya Harusawa
- Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences
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3
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Waugh B, Ghosh A, Bhattacharyya D, Ghoshal N, Banerjee R. In silico work flow for scaffold hopping in Leishmania. BMC Res Notes 2014; 7:802. [PMID: 25399834 PMCID: PMC4247209 DOI: 10.1186/1756-0500-7-802] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/29/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Leishmaniasis,a broad spectrum of diseases caused by several sister species of protozoa belonging to family trypanosomatidae and genus leishmania , generally affects poorer sections of the populace in third world countries. With the emergence of strains resistant to traditional therapies and the high cost of second line drugs which generally have severe side effects, it becomes imperative to continue the search for alternative drugs to combat the disease. In this work, the leishmanial genomes and the human genome have been compared to identify proteins unique to the parasite and whose structures (or those of close homologues) are available in the Protein Data Bank. Subsequent to the prioritization of these proteins (based on their essentiality, virulence factor etc.), inhibitors have been identified for a subset of these prospective drug targets by means of an exhaustive literature survey. A set of three dimensional protein-ligand complexes have been assembled from the list of leishmanial drug targets by culling structures from the Protein Data Bank or by means of template based homology modeling followed by ligand docking with the GOLD software. Based on these complexes several structure based pharmacophores have been designed and used to search for alternative inhibitors in the ZINC database. RESULT This process led to a list of prospective compounds which could serve as potential antileishmanials. These small molecules were also used to search the Drug Bank to identify prospective lead compounds already in use as approved drugs. Interestingly, paromomycin which is currently being used as an antileishmanial drug spontaneously appeared in the list, probably giving added confidence to the 'scaffold hopping' computational procedures adopted in this work. CONCLUSIONS The report thus provides the basis to experimentally verify several lead compounds for their predicted antileishmanial activity and includes several useful data bases of prospective drug targets in leishmania, their inhibitors and protein--inhibitor three dimensional complexes.
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Affiliation(s)
- Barnali Waugh
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
| | - Ambarnil Ghosh
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
| | - Dhananjay Bhattacharyya
- />Computer Science Division, Saha Institute of Nuclear Physics, Sector-1, Block AF, Biddhannagar, Kolkata, 700064 India
| | - Nanda Ghoshal
- />Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Rahul Banerjee
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
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4
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Kotsuki H, Moritaka M, Nakano K. Efficient Organocatalytic Michael Addition Reaction of β−Ketoesters under High Pressure. HETEROCYCLES 2013. [DOI: 10.3987/com-13-12818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Sirci F, Istyastono EP, Vischer HF, Kooistra AJ, Nijmeijer S, Kuijer M, Wijtmans M, Mannhold R, Leurs R, de Esch IJP, de Graaf C. Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. J Chem Inf Model 2012; 52:3308-24. [DOI: 10.1021/ci3004094] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Francesco Sirci
- Laboratory for Chemometrics
and Chemoinformatics, Chemistry Department, University of Perugia, Via Elce di Sotto, 10, I-06123 Perugia Italy
| | - Enade P. Istyastono
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Molecular Modeling Division, Pharmaceutical
Technology Laboratory, Universitas Sanata Dharma, Yogyakarta, Indonesia
| | - Henry F. Vischer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Albert J. Kooistra
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Saskia Nijmeijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Martien Kuijer
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Raimund Mannhold
- Department of Laser Medicine,
Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Rob Leurs
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry,
Faculty of Sciences, Amsterdam Institute for Molecules, Medicines
and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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6
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Istyastono EP, Nijmeijer S, Lim HD, van de Stolpe A, Roumen L, Kooistra AJ, Vischer HF, de Esch IJP, Leurs R, de Graaf C. Molecular determinants of ligand binding modes in the histamine H(4) receptor: linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies. J Med Chem 2011; 54:8136-47. [PMID: 22003888 DOI: 10.1021/jm201042n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The histamine H(4) receptor (H(4)R) is a G protein-coupled receptor (GPCR) that plays an important role in inflammation. Similar to the homologous histamine H(3) receptor (H(3)R), two acidic residues in the H(4)R binding pocket, D(3.32) and E(5.46), act as essential hydrogen bond acceptors of positively ionizable hydrogen bond donors in H(4)R ligands. Given the symmetric distribution of these complementary pharmacophore features in H(4)R and its ligands, different alternative ligand binding mode hypotheses have been proposed. The current study focuses on the elucidation of the molecular determinants of H(4)R-ligand binding modes by combining (3D) quantitative structure-activity relationship (QSAR), protein homology modeling, molecular dynamics simulations, and site-directed mutagenesis studies. We have designed and synthesized a series of clobenpropit (N-(4-chlorobenzyl)-S-[3-(4(5)-imidazolyl)propyl]isothiourea) derivatives to investigate H(4)R-ligand interactions and ligand binding orientations. Interestingly, our studies indicate that clobenpropit (2) itself can bind to H(4)R in two distinct binding modes, while the addition of a cyclohexyl group to the clobenpropit isothiourea moiety allows VUF5228 (5) to adopt only one specific binding mode in the H(4)R binding pocket. Our ligand-steered, experimentally supported protein modeling method gives new insights into ligand recognition by H(4)R and can be used as a general approach to elucidate the structure of protein-ligand complexes.
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Affiliation(s)
- Enade P Istyastono
- Department of Pharmacochemistry, Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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7
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Berlin M, Boyce CW, de Lera Ruiz M. Histamine H3 Receptor as a Drug Discovery Target. J Med Chem 2010; 54:26-53. [DOI: 10.1021/jm100064d] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michael Berlin
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Christopher W. Boyce
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Manuel de Lera Ruiz
- Chemical Research, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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8
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Ruthenium complexes endowed with potent anti-Trypanosoma cruzi activity: Synthesis, biological characterization and structure–activity relationships. Bioorg Med Chem 2009; 17:5038-43. [DOI: 10.1016/j.bmc.2009.05.071] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/25/2009] [Accepted: 05/27/2009] [Indexed: 01/07/2023]
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9
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Lim HD, Istyastono EP, van de Stolpe A, Romeo G, Gobbi S, Schepers M, Lahaye R, Menge WM, Zuiderveld OP, Jongejan A, Smits RA, Bakker RA, Haaksma EE, Leurs R, de Esch IJ. Clobenpropit analogs as dual activity ligands for the histamine H3 and H4 receptors: Synthesis, pharmacological evaluation, and cross-target QSAR studies. Bioorg Med Chem 2009; 17:3987-94. [DOI: 10.1016/j.bmc.2009.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 04/01/2009] [Accepted: 04/06/2009] [Indexed: 11/29/2022]
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10
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Tanrikulu Y, Schneider G. Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nat Rev Drug Discov 2008; 7:667-77. [DOI: 10.1038/nrd2615] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Wijtmans M, Celanire S, Snip E, Gillard MR, Gelens E, Collart PP, Venhuis BJ, Christophe B, Hulscher S, van der Goot H, Lebon F, Timmerman H, Bakker RA, Lallemand BILF, Leurs R, Talaga PE, de Esch IJP. 4-benzyl-1H-imidazoles with oxazoline termini as histamine H3 receptor agonists. J Med Chem 2008; 51:2944-53. [PMID: 18433114 DOI: 10.1021/jm7014149] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Research on the therapeutic applications of the histamine H3 receptor (H3R) has traditionally focused on antagonists/inverse agonists. In contrast, H3R agonists have received less attention despite their potential use in several disease areas. The lower availability of H3R agonists not only hampers their full therapeutic exploration, it also prevents an unequivocal understanding of the structural requirements for H3R activation. In the light of these important issues, we present our findings on 4-benzyl-1H-imidazole-based H3R agonists. Starting from two high throughput screen hits (10 and 11), the benzyl side chain was altered with lipophilic groups using combinatorial and classical chemical approaches (compounds 12-31). Alkyne- or oxazolino-substituents gave excellent affinities and agonist activities up to the single digit nM range. Our findings further substantiate the growing notion that basic ligand sidechains are not necessary for H 3R activation and reveal the oxazolino group as a hitherto unexplored functional group in H3R research.
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Affiliation(s)
- Maikel Wijtmans
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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12
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Schlegel B, Laggner C, Meier R, Langer T, Schnell D, Seifert R, Stark H, Höltje HD, Sippl W. Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening. J Comput Aided Mol Des 2007; 21:437-53. [PMID: 17668276 DOI: 10.1007/s10822-007-9127-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 06/29/2007] [Indexed: 10/23/2022]
Abstract
The human histamine H(3) receptor (hH(3)R) is a G-protein coupled receptor (GPCR), which modulates the release of various neurotransmitters in the central and peripheral nervous system and therefore is a potential target in the therapy of numerous diseases. Although ligands addressing this receptor are already known, the discovery of alternative lead structures represents an important goal in drug design. The goal of this work was to study the hH(3)R and its antagonists by means of molecular modelling tools. For this purpose, a strategy was pursued in which a homology model of the hH(3)R based on the crystal structure of bovine rhodopsin was generated and refined by molecular dynamics simulations in a dipalmitoylphosphatidylcholine (DPPC)/water membrane mimic before the resulting binding pocket was used for high-throughput docking using the program GOLD. Alternatively, a pharmacophore-based procedure was carried out where the alleged bioactive conformations of three different potent hH(3)R antagonists were used as templates for the generation of pharmacophore models. A pharmacophore-based screening was then carried out using the program Catalyst. Based upon a database of 418 validated hH(3)R antagonists both strategies could be validated in respect of their performance. Seven hits obtained during this screening procedure were commercially purchased, and experimentally tested in a [(3)H]N(alpha)-methylhistamine binding assay. The compounds tested showed affinities at hH(3)R with K ( i ) values ranging from 0.079 to 6.3 muM.
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Affiliation(s)
- Birgit Schlegel
- Institute of Pharmaceutical Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr 1, 40197, Dusseldorf, Germany
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13
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Wijtmans M, Leurs R, de Esch I. Histamine H3 receptor ligands break ground in a remarkable plethora of therapeutic areas. Expert Opin Investig Drugs 2007; 16:967-85. [PMID: 17594183 DOI: 10.1517/13543784.16.7.967] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The neurotransmitter histamine exerts its action through four distinct histamine receptors. The histamine H(1) and H(2) receptor are well established drug targets, whereas the histamine H(4) receptor is undergoing rigorous characterisation at present. The histamine H(3) receptor (H(3)R) is a G(i/o)-protein coupled receptor and is mostly expressed in the CNS. A remarkably large and different array of therapeutic areas, in which ligands for the H(3)R may prove useful, has been identified and a massive research undertaking is underway to substantiate the high expectations for H(3)R ligands. At present, several ligands for the H(3)R are being evaluated in clinical studies. In this review, the many potential therapeutic areas for H(3)R antagonists, inverse agonists and agonists is discussed. Promising medicinal chemistry and toxicological developments, as well as the advancement of several H(3)R ligands into the clinic, will be highlighted. This review also describes the problems that have been overcome and the questions that remain in developing H(3)R-related drugs. Considering the tremendous efforts by industry, it can be expected that the first H(3)R drugs will reach the market soon.
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Affiliation(s)
- Maikel Wijtmans
- Vrije Universiteit Amsterdam, Leiden/Amsterdam Center of Drug Research, Division of Medicinal Chemistry, Faculty of Sciences, De Boelelaan 1083, Amsterdam, The Netherlands
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14
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Roche O, Rodríguez Sarmiento RM. A new class of histamine H3 receptor antagonists derived from ligand based design. Bioorg Med Chem Lett 2007; 17:3670-5. [PMID: 17498953 DOI: 10.1016/j.bmcl.2007.04.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 04/13/2007] [Accepted: 04/15/2007] [Indexed: 11/21/2022]
Abstract
Design and synthesis of highly potent and selective non-imidazole inverse agonists for the histamine H(3) receptor is described. The study validates a new pharmacophore model based on the merging of two previously described models. It also demonstrates that the removal of the basic center potentially interacting with ASP3.32 and common to both models leads to loss of activity, whereas the replacement of the second basic center by an acceptor retains the potency.
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Affiliation(s)
- Olivier Roche
- F. Hoffmann-La Roche Ltd, Pharmaceutical Research Basel, Discovery Chemistry, CH-4070 Basel, Switzerland
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15
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Narkhede S, Degani M. Pharmacophore Refinement and 3D-QSAR Studies of Histamine H3 Antagonists. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200610144] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Howard HR. Fused thiazole derivatives having affinity for the histamine H3receptor. Expert Opin Ther Pat 2007. [DOI: 10.1517/13543776.17.1.129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Affiliation(s)
- Steffen Renner
- Institute of Organic Chemistry & Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt, Germany
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18
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Axe FU, Bembenek SD, Szalma S. Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore. J Mol Graph Model 2006; 24:456-64. [PMID: 16386444 DOI: 10.1016/j.jmgm.2005.10.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 10/03/2005] [Accepted: 10/03/2005] [Indexed: 10/25/2022]
Abstract
Molecular modeling was used to analyze the binding mode and activities of histamine H3 receptor antagonists. A model of the H3 receptor was constructed through homology modeling methods based on the crystal structure of bovine rhodopsin. Known H3 antagonists were interactively docked into the putative antagonist binding pocket and the resultant model was subjected to molecular mechanics energy minimization and molecular dynamics simulations which included a continuum model of the lipid bilayer and intra- and extracellular aqueous environments surrounding the transmembrane helices. The transmembrane helices stayed well embedded in the dielectric slab representing the lipid bilayer and the intra- and extracellular loops remain situated in the aqueous solvent region of the model during molecular dynamics simulations of up to 200 ps in duration. A pharmacophore model was calculated by mapping the features common to three active compounds three-dimensionally in space. The 3D pharmacophore model complements our atomistic receptor/ligand modeling. The H3 antagonist pharmacophore consists of two protonation sites (i.e. basic centers) connected by a central aromatic ring or hydrophobic region. These two basic sites can simultaneously interact with Asp 114 (3.32) in helix III and a Glu 206 (5.46) in helix V which are believed to be the key residues that histamine interacts with to stabilize the receptor in the active state. The interaction with Glu 206 is consistent with the enhanced activity resulting from the additional basic site. In addition to these two salt bridging interactions, the central region of these antagonists contains a lipophilic group, usually an aromatic ring, that is found to interact with several nearby hydrophobic side chains. The picture of antagonist binding provided by these models is consistent with earlier pharmacophore models for H3 antagonists with some exceptions.
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Affiliation(s)
- Frank U Axe
- Axe Consulting Services, 14595 Surrey Junction Lane, Sutter Creek, CA 95685, USA.
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19
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Letavic MA, Barbier AJ, Dvorak CA, Carruthers NI. Recent medicinal chemistry of the histamine H3 receptor. PROGRESS IN MEDICINAL CHEMISTRY 2006; 44:181-206. [PMID: 16697898 DOI: 10.1016/s0079-6468(05)44405-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Michael A Letavic
- Johnson and Johnson Pharmaceutical Research and Development LLC, San Diego, CA 92121, USA
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20
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Vaccaro WD, Sher R, Berlin M, Shih NY, Aslanian R, Schwerdt JH, McCormick KD, Piwinski JJ, West RE, Anthes JC, Williams SM, Wu RL, She HS, Rivelli MA, Mutter JC, Corboz MR, Hey JA, Favreau L. Novel histamine H3 receptor antagonists based on the 4-[(1H-imidazol-4-yl)methyl]piperidine scaffold. Bioorg Med Chem Lett 2006; 16:395-9. [PMID: 16246552 DOI: 10.1016/j.bmcl.2005.09.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 09/17/2005] [Accepted: 09/26/2005] [Indexed: 11/16/2022]
Abstract
We report the discovery of novel histamine H(3) receptor antagonists based on 4-[(1H-imidazol-4-yl)methyl]piperidine. The most potent compounds in the series (e.g., 7) result from the attachment of a substituted aniline amide to the main pharmacophore piperidine via a two-methylene linker.
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Affiliation(s)
- Wayne D Vaccaro
- The Schering Plough Research Institute, 2015 Galloping Hill Rd., Kenilworth, NJ 07033, USA
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21
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Lorenzi S, Mor M, Bordi F, Rivara S, Rivara M, Morini G, Bertoni S, Ballabeni V, Barocelli E, Plazzi PV. Validation of a histamine H3 receptor model through structure-activity relationships for classical H3 antagonists. Bioorg Med Chem 2005; 13:5647-57. [PMID: 16085419 DOI: 10.1016/j.bmc.2005.05.072] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2005] [Indexed: 10/25/2022]
Abstract
Histamine H(3) receptor is a G protein-coupled receptor whose activation inhibits the synthesis and release of histamine and other neurotransmitters from nerve endings and is involved in the modulation of different central nervous system functions. H(3) antagonists have been proposed for their potential usefulness in diseases characterized by impaired neurotransmission and they have demonstrated beneficial effects on learning and food intake in animal models. In the present work, a 3D model of the rat histamine H(3) receptor, built by comparative modeling from the crystallographic coordinates of bovine rhodopsin, is presented with the discussion of its ability to predict the potency of known and new H(3) antagonists. A putative binding site for classical, imidazole-derived H(3) antagonists was identified by molecular docking. Comparison with a known pharmacophore model and the binding affinity of a new rigid H(3) antagonist (compound 1, pK(i)=8.02) allowed the characterization of a binding scheme which could also account for the different affinities observed in a recently reported series of potent H(3) antagonists, characterized by a 2-aminobenzimidazole moiety. Molecular dynamics simulations were employed to assess the stability and reliability of the proposed binding mode. Two new conformationally constrained benzimidazole derivatives were prepared and their binding affinity was tested on rat brain membranes; compound 9, designed to reproduce the conformation of a known potent H(3) antagonist, showed higher potency than compound 8, as expected from the binding scheme hypothesized.
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Affiliation(s)
- Simone Lorenzi
- Dipartimento Farmaceutico, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43100 Parma, Italy
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22
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Kitbunnadaj R, Hoffmann M, Fratantoni SA, Bongers G, Bakker RA, Wieland K, el Jilali A, De Esch IJP, Menge WMPB, Timmerman H, Leurs R. New high affinity H3 receptor agonists without a basic side chain. Bioorg Med Chem 2005; 13:6309-23. [PMID: 16213736 DOI: 10.1016/j.bmc.2005.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 05/02/2005] [Accepted: 05/06/2005] [Indexed: 11/16/2022]
Abstract
In this study, we replaced the basic amine function of the known histamine H(3) receptor agonists imbutamine or immepip with non-basic alcohol or hydrocarbon moieties. All compounds in this study show a moderate to high affinity for the cloned human H(3) receptor and, unexpectedly, almost all of them act as potent agonists. Moreover, in the alcohol series, we consistently observed an increased selectivity for the human H(3) receptor over the human H(4) receptor, but none of the compounds in this series possess increased affinity and functional activity compared to their alkylamine congeners. In this new series of compounds VUF5657, 5-(1H-imidazol-4-yl)-pentan-1-ol, is the most potent histamine H(3) receptor agonist (pK(i) = 8.0 and pEC(50) = 8.1) with a 320-fold selectivity at the human H(3) receptor over the human H(4) receptor.
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Affiliation(s)
- Ruengwit Kitbunnadaj
- Leiden/Amsterdam Center of Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Chemistry, Vrije Universiteit Amsterdam, The Netherlands
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23
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Leurs R, Bakker RA, Timmerman H, de Esch IJP. The histamine H3 receptor: from gene cloning to H3 receptor drugs. Nat Rev Drug Discov 2005; 4:107-20. [PMID: 15665857 DOI: 10.1038/nrd1631] [Citation(s) in RCA: 392] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Since the cloning of the histamine H(3) receptor cDNA in 1999 by Lovenberg and co-workers, this histamine receptor has gained the interest of many pharmaceutical companies as a potential drug target for the treatment of various important disorders, including obesity, attention-deficit hyperactivity disorder, Alzheimer's disease, schizophrenia, as well as for myocardial ischaemia, migraine and inflammatory diseases. Here, we discuss relevant information on this target protein and describe the development of various H(3) receptor agonists and antagonists, and their effects in preclinical animal models.
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Affiliation(s)
- Rob Leurs
- Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Vrije Universiteit Amsterdam, Faculty of Science, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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24
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Abstract
The aim of scaffold hopping is to discover structurally novel compounds starting from known active compounds by modifying the central core structure of the molecule. Scaffold hopping is a central task of modern medicinal chemistry requiring a multitude of techniques, which are discussed in this article. Their application has led to several molecules with chemically completely different core structures, and yet binding to the same receptor. Computational approaches for scaffold hopping highlight the challenges of the field that are still unsolved.:
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Affiliation(s)
- Hans-Joachim Böhm
- Molecular Structure and Design, Pharmaceuticals Division, F. Hoffmann-La Roche AG, PRBD-CS, Building 092/3.56B, CH-4070 Basel, Switzerland
| | - Alexander Flohr
- Molecular Structure and Design, Pharmaceuticals Division, F. Hoffmann-La Roche AG, PRBD-CS, Building 092/3.56B, CH-4070 Basel, Switzerland
| | - Martin Stahl
- Molecular Structure and Design, Pharmaceuticals Division, F. Hoffmann-La Roche AG, PRBD-CS, Building 092/3.56B, CH-4070 Basel, Switzerland.
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25
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Bleicher KH, Green LG, Martin RE, Rogers-Evans M. Ligand identification for G-protein-coupled receptors: a lead generation perspective. Curr Opin Chem Biol 2004; 8:287-96. [PMID: 15183327 DOI: 10.1016/j.cbpa.2004.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This review addresses strategies for the generation of ligands for G-protein-coupled receptors outside classical high-throughput screening and literature based approaches. These range from the chemical intuition-based strategies of endogenous ligand elaboration and privileged structure decoration to the in silico approaches of virtual screening and de novo design. Examples are cited where supporting pharmacological data has been presented.
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Affiliation(s)
- Konrad H Bleicher
- F Hoffmann-La Roche Ltd, Pharmaceuticals Division, Lead Generation, PRBD-CI, Bldg 65/410, CH-4070 Basel, Switzerland.
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26
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Mikó T, Ligneau X, Pertz HH, Arrang JM, Ganellin CR, Schwartz JC, Schunack W, Stark H. Structural variations of 1-(4-(phenoxymethyl)benzyl)piperidines as nonimidazole histamine H3 receptor antagonists. Bioorg Med Chem 2004; 12:2727-36. [PMID: 15110854 DOI: 10.1016/j.bmc.2004.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2003] [Accepted: 03/05/2004] [Indexed: 10/26/2022]
Abstract
Recent bioisoteric replacements in histamine H3 receptor ligands with an exchange of the imidazole moiety by a piperidino group as well as of the trimethylene chain in 4-((3-phenoxy)propyl)-lH-imidazole derivatives (proxifan class) by an alpha,alpha'-xylendiyl linker represents the starting point in the development of 1-(4-(phenoxymethyl)benzyl)piperidines as a new class of nonimidazole histamine H3 receptor antagonists. According to different strategies in optimization of imidazole-containing antagonists the central benzyl phenyl ether moiety was replaced by numerous other polar functionalities. Additionally, the ortho- and meta-analogues of the lead were synthesized to determine the influence of the position of the piperidinomethyl substituent. The new compounds were tested in an in vitro binding assay for their affinities for cloned human H3 receptors stably expressed in CHO-K1 cells and for their oral in vivo potencies brain in a functional screening assay in the brain of mice. Additionally, activities of selected compounds were determined in the guinea-pig ileum functional test model. In contrast to the analogues ortho-substituted compounds all other compounds maintained respectable affinities for the human H3 receptor (-log Ki values 6.3-7.5). Despite the results from other classes of compounds the 4-methyl substituted derivatives generally displayed higher affinities than the corresponding 4-chloro substituted compounds. In vivo only the inverse phenyl benzyl ether (3) showed worthwhile antagonist potencies.
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Affiliation(s)
- Tibor Mikó
- Institut für Pharmazie, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin, Germany
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27
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Lloyd DG, Buenemann CL, Todorov NP, Manallack DT, Dean PM. Scaffold Hopping in De Novo Design. Ligand Generation in the Absence of Receptor Information. J Med Chem 2004; 47:493-6. [PMID: 14736231 DOI: 10.1021/jm034222u] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the de novo generation of chemotypes and scaffolds for the estrogen receptor, without use of the receptor structure in the assembly phase. Through use of ligand superpositions or a single bound conformation of a known active, a pseudoreceptor can be generated as a design envelope, within which novel structures are readily assembled. Many of these structures have high similarity to known chemotypes. Scaffold hopping is readily achieved within this pseudoreceptor, indicating the advantages of such an approach in discovery research.
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Affiliation(s)
- David G Lloyd
- De Novo Pharmaceuticals, Compass House, Vision Park Histon, Cambridge, CB4 9ZR, UK.
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28
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Bertsch M, Kassner RJ. Selective Staining of Proteins with Hydrophobic Surface Sites on a Native Electrophoretic Gel. J Proteome Res 2003; 2:469-75. [PMID: 14582643 DOI: 10.1021/pr025579+] [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: 11/28/2022]
Abstract
Chemical proteomics aims to characterize all of the proteins in the proteome with respect to their function, which is associated with their interaction with other molecules. We propose the identification of a subproteomic library of expressed proteins whose native structures are typified by the presence of hydrophobic surface sites, which are often involved in interactions with small molecules, membrane lipids, and other proteins, pertaining to their functions. We demonstrate that soluble globular proteins with hydrophobic surface sites can be detected selectively by staining on an electrophoretic gel run under nondenaturing conditions. The application of these staining techniques may help elucidate new catalytic, transport, and regulatory functionalities in complex proteomic screenings.
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Affiliation(s)
- Martina Bertsch
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Suite 4500, Chicago, Illinois 60607, USA
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29
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Turner SC, Esbenshade TA, Bennani YL, Hancock AA. A new class of histamine H(3)-receptor antagonists: synthesis and structure-activity relationships of 7,8,9,10-tetrahydro-6H-cyclohepta[b]quinolines. Bioorg Med Chem Lett 2003; 13:2131-5. [PMID: 12798320 DOI: 10.1016/s0960-894x(03)00356-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The synthesis and biological evaluation of novel cycloheptaquinoline antagonists of the human H(3) receptor are described. Two series of compounds, bearing either an amino substituent or an alkyne linker at the 11-position, were investigated. Modifications of the amino substituents, optimization of chain length and the effect of conformational restraints are described. Several compounds with high affinity and selectivity for the H(3) receptor were discovered.
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Affiliation(s)
- Sean C Turner
- Neuroscience Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, 60064, Abbott Park, IL, USA.
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30
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Vasudevan A, Conner SE, Gentles RG, Faghih R, Liu H, Dwight W, Ireland L, Kang CH, Esbenshade TA, Bennani YL, Hancock AA. Synthesis and evaluation of potent pyrrolidine H(3) antagonists. Bioorg Med Chem Lett 2002; 12:3055-8. [PMID: 12372500 DOI: 10.1016/s0960-894x(02)00685-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The synthesis and biological evaluation of novel antagonists of the rat H(3) receptor are described. These compounds differ from prototypical H(3) antagonists in that they do not contain an imidazole moiety, but rather a substituted aminopyrrolidine moiety. A systematic modification of the substituents on the aminopyrrolidine ring was performed using pre-formatted precursor sets, where applicable, to afford several compounds with high affinity and selectivity for the H(3) receptor.
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Affiliation(s)
- Anil Vasudevan
- Neuroscience Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60031, USA.
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31
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Ting P, Lee J, Albanese M, Tom W, Solomon D, Aslanian R, Shih N, West R. The synthesis of substituted fluorenes as novel non-imidazole histamine h(3) inhibitors. Bioorg Med Chem Lett 2002; 12:2643-6. [PMID: 12182878 DOI: 10.1016/s0960-894x(02)00521-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A novel non-imidazole fluorene oxime 1a has been identified as a histamine H(3) inhibitor, and its structure-activity relationship has been evaluated.
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Affiliation(s)
- Pauline Ting
- The Schering Plough Research Institute, 2015 Galloping Hill Road, 07033, Kenilworth, NJ, USA.
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32
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Abstract
Chemical genomics represents a convergence of biology and chemistry in the era of global approaches to target identification and intervention. The success of genomics has led to a bottleneck in target validation that could be overcome by using small diverse organic compounds to interfere with biological processes. Because of the limitations of existing compound collections, this diversity can only fully be exploited using in silico design techniques to guide the selection of molecules with optimal binding properties. Structure-based design is used to create structures de novo that can be synthesized for use as chemical probes and drug leads.
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Affiliation(s)
- Edward D Zanders
- De Nove Pharmaceuticals, Compass House, Vision Park, Histon, Cambridge, UK CB4 9ZR.
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33
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Aslanian R, Mutahi MW, Shih NY, McCormick KD, Piwinski JJ, Ting PC, Albanese MM, Berlin MY, Zhu X, Wong SC, Rosenblum SB, Jiang Y, West R, She S, Williams SM, Bryant M, Hey JA. Identification of a novel, orally bioavailable histamine H(3) receptor antagonist based on the 4-benzyl-(1H-imidazol-4-yl) template. Bioorg Med Chem Lett 2002; 12:937-41. [PMID: 11958998 DOI: 10.1016/s0960-894x(02)00055-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A novel series of histamine H(3) receptor antagonists, based on the 4-benzyl-(1H-imidazole-4-yl) template, incorporating urea and carbamate linkers has been prepared. Compound 3j is a selective H(3) antagonist and demonstrates excellent oral plasma levels in the rat and monkey.
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Affiliation(s)
- Robert Aslanian
- The Schering Plough Research Institute, Kenilworth, NJ 07033, USA.
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