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Assis DB, Aragão Neto HDC, da Fonsêca DV, de Andrade HHN, Braga RM, Badr N, Maia MDS, Castro RD, Scotti L, Scotti MT, de Almeida RN. Antinociceptive Activity of Chemical Components of Essential Oils That Involves Docking Studies: A Review. Front Pharmacol 2020; 11:777. [PMID: 32547391 PMCID: PMC7272657 DOI: 10.3389/fphar.2020.00777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION Pain is considered an unpleasant sensory and emotional experience, being considered as one of the most important causes of human suffering. Computational chemistry associated with bioinformatics has stood out in the process of developing new drugs, through natural products, to manage this condition. OBJECTIVE To analyze, through literature data, recent molecular coupling studies on the antinociceptive activity of essential oils and monoterpenes. DATA SOURCE Systematic search of the literature considering the years of publications between 2005 and December 2019, in the electronic databases PubMed and Science Direct. ELIGIBILITY CRITERIA Were considered as criteria of 1) Biological activity: non-clinical effects of an OE and/or monoterpenes on antinociceptive activity based on animal models and in silico analysis, 2) studies with plant material: chemically characterized essential oils and/or their constituents isolated, 3) clinical and non-clinical studies with in silico analysis to assess antinociceptive activity, 4) articles published in English. Exclusion criteria were literature review, report or case series, meta-analysis, theses, dissertations, and book chapter. RESULTS Of 16,006 articles, 16 articles fulfilled all the criteria. All selected studies were non-clinical. The most prominent plant families used were Asteraceae, Euphorbiaceae, Verbenaceae, Lamiaceae, and Lauraceae. Among the phytochemicals studied were α-Terpineol, 3-(5-substituted-1,3,4-oxadiazol-2-yl)-N'-[2-oxo-1,2-dihydro-3H-indol-3-ylidene] propane hydrazide, β-cyclodextrin complexed with citronellal, (-)-α-bisabolol, β-cyclodextrin complexed with farnesol, and p-Cymene. The softwares used for docking studies were Molegro Virtual Docker, Sybyl®X, Vlife MDS, AutoDock Vina, Hex Protein Docking, and AutoDock 4.2 in PyRx 0.9. The molecular targets/complexes used were Nitric Oxide Synthase, COX-2, GluR2-S1S2, TRPV1, β-CD complex, CaV1, CaV2.1, CaV2.2, and CaV2.3, 5-HT receptor, delta receptor, kappa receptor, and MU (μ) receptor, alpha adrenergic, opioid, and serotonergic receptors, muscarinic receptors and GABAA opioid and serotonin receptors, 5-HT3 and M2 receptors. Many of the covered studies used molecular coupling to investigate the mechanism of action of various compounds, as well as molecular dynamics to investigate the stability of protein-ligand complexes. CONCLUSIONS The studies revealed that through the advancement of more robust computational techniques that complement the experimental studies, they may allow some notes on the identification of a new candidate molecule for therapeutic use.
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Affiliation(s)
- Davidson Barbosa Assis
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | | | - Diogo Vilar da Fonsêca
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Humberto Hugo Nunes de Andrade
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Renan Marinho Braga
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Nader Badr
- First Faculty of Medicine, Charles University, Prague, Czechia
| | - Mayara dos Santos Maia
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Ricardo Dias Castro
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Luciana Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Marcus Tullius Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
| | - Reinaldo Nóbrega de Almeida
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, João Pessoa, Brazil
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Lee JH, Seo SH, Lim EJ, Cho NC, Nam G, Kang SB, Pae AN, Jeong N, Keum G. Synthesis and biological evaluation of 1-(isoxazol-5-ylmethylaminoethyl)-4-phenyl tetrahydropyridine and piperidine derivatives as potent T-type calcium channel blockers with antinociceptive effect in a neuropathic pain model. Eur J Med Chem 2014; 74:246-57. [DOI: 10.1016/j.ejmech.2013.12.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/20/2013] [Accepted: 12/24/2013] [Indexed: 12/11/2022]
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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Leach AG. Predicting the activity and toxicity of new psychoactive substances: a pharmaceutical industry perspective. Drug Test Anal 2013; 6:739-45. [DOI: 10.1002/dta.1593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Andrew G. Leach
- Liverpool John Moores University; James Parsons Building, Byrom Street Liverpool L3 3AF UK
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Choi KH. The design and discovery of T-type calcium channel inhibitors for the treatment of central nervous system disorders. Expert Opin Drug Discov 2013; 8:919-31. [DOI: 10.1517/17460441.2013.796926] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists. J Comput Aided Mol Des 2013; 27:305-19. [PMID: 23625023 DOI: 10.1007/s10822-013-9647-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/13/2013] [Indexed: 01/08/2023]
Abstract
The α1-adrenoceptors (α1-ARs), in particular the α1A-AR subtype, are current therapeutic targets of choice for the treatment of urogenital conditions, such as benign prostatic hyperplasia (BPH). Due to the similarity between the transmembrane domains of the α1-AR subtypes, and the serotonin receptor subtype 1A (5-HT1A-R), currently used α1-AR subtype-selective drugs to treat BPH display considerable off-target affinity for the 5-HT1A-R, leading to side effects. We describe the construction and validation of pharmacophores for 5-HT1A-R agonists and antagonists. Through the structural diversity of the training sets used in their development, these pharmacophores define the properties of a compound needed to bind to 5-HT1A receptors. Using these and previously published pharmacophores in virtual screening and profiling, we have identified unique chemical compounds (hits) that fit the requirements to bind to our target, the α1A-AR, selectively over the off-target, the 5-HT1A-R. Selected hits have been obtained and their affinities for α1A-AR, α1B-AR and 5-HT1A-R determined in radioligand binding assays, using membrane preparations which contain human receptors expressed individually. Three of the tested hits demonstrate statistically significant selectivity for α1A-AR over 5-HT1A-R. All seven tested hits bind to α1A-AR, with two compounds displaying K i values below 1 μM, and a further two K i values of around 10 μM. The insights and knowledge gained through the development of the new 5-HT1A-R pharmacophores will greatly aid in the design and synthesis of derivatives of our lead compound, and allow the generation of more efficacious and selective ligands.
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Park JE, Ji WK, Jang JW, Pae AN, Choi K, Choi KH, Kang J, Roh EJ. Synthesis and biological evaluation of 1-(2-hydroxy-3-phenyloxypropyl)piperazine derivatives as T-type calcium channel blockers. Bioorg Med Chem Lett 2013; 23:1887-90. [DOI: 10.1016/j.bmcl.2012.12.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/10/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
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Gurdal EE, Durmaz I, Cetin-Atalay R, Yarim M. Synthesis and cytotoxicity studies of novel benzhydrylpiperazine carboxamide and thioamide derivatives. J Enzyme Inhib Med Chem 2013; 29:205-14. [DOI: 10.3109/14756366.2013.765416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Enise Ece Gurdal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University
Kayisdagi, IstanbulTurkey
| | - Irem Durmaz
- Department of Molecular Biology and Genetics, BilGen, Genetics and Biotechnology Research Center, Faculty of Science, Bilkent University
Bilkent, AnkaraTurkey
| | - Rengul Cetin-Atalay
- Department of Molecular Biology and Genetics, BilGen, Genetics and Biotechnology Research Center, Faculty of Science, Bilkent University
Bilkent, AnkaraTurkey
| | - Mine Yarim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University
Kayisdagi, IstanbulTurkey
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Watanuki S, Matsuura K, Tomura Y, Okada M, Okazaki T, Ohta M, Tsukamoto SI. Synthesis and pharmacological evaluation of 1-alkyl-N-[(1R)-1-(4-fluorophenyl)-2-methylpropyl]piperidine-4-carboxamide derivatives as novel antihypertensive agents. Chem Pharm Bull (Tokyo) 2012; 59:1376-85. [PMID: 22041074 DOI: 10.1248/cpb.59.1376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We synthesized and evaluated inhibitory activity against T-type Ca(2+) channels for a series of 1-alkyl-N-[(1R)-1-(4-fluorophenyl)-2-methylpropyl]piperidine-4-carboxamide derivatives. Structure-activity relationship studies have revealed that the isopropyl substituent at the benzylic position plays an important role in exerting potent inhibitory activity, and the absolute configuration of the benzylic position was found to be opposite that of mibefradil, which was first launched as a new class of T-type Ca(2+) channel blocker. Oral administration of N-[(1R)-1-(4-fluorophenyl)-2-methylpropyl]-1-[2-(3-methoxyphenyl)ethyl]piperidine-4-carboxamide (17f) lowered blood pressure in spontaneously hypertensive rats without inducing reflex tachycardia, an adverse effect often caused by traditional L-type Ca(2+) channel blockers.
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Affiliation(s)
- Susumu Watanuki
- Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305–8585, Japan.
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Watanuki S, Matsuura K, Tomura Y, Okada M, Okazaki T, Ohta M, Tsukamoto SI. Synthesis and Pharmacological Evaluation of 2-(1-Alkylpiperidin-4-yl)-N-[(1R)-1-(4-fluorophenyl)-2-methylpropyl]acetamide Derivatives as Novel Antihypertensive Agents. Chem Pharm Bull (Tokyo) 2012; 60:223-34. [DOI: 10.1248/cpb.60.223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Synthesis and biological evaluation of 4-piperidinecarboxylate and 4-piperidinecyanide derivatives for T-type calcium channel blockers. Bioorg Med Chem Lett 2011; 21:5910-5. [DOI: 10.1016/j.bmcl.2011.07.087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/07/2011] [Accepted: 07/23/2011] [Indexed: 11/24/2022]
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Ripphausen P, Wassermann AM, Bajorath J. REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications. J Chem Inf Model 2011; 51:2467-73. [DOI: 10.1021/ci200309j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Peter Ripphausen
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Anne Mai Wassermann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
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Synthesis and pharmacological evaluation of 1-alkyl-N-[2-ethyl-2-(4-fluorophenyl)butyl]piperidine-4-carboxamide derivatives as novel antihypertensive agents. Bioorg Med Chem 2011; 19:5628-38. [DOI: 10.1016/j.bmc.2011.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/15/2011] [Accepted: 07/16/2011] [Indexed: 11/18/2022]
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Ullapu PR, Ku SJ, Choi YH, Park JY, Han SY, Baek DJ, Lee JK, Pae AN, Min SJ, Cho YS. Synthesis and Biological Evaluation of 1-Heteroarylmethyl 1,4-Diazepanes Derivatives as Potential T-type Calcium Channel Blockers. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.8.3063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Reger TS, Yang ZQ, Schlegel KAS, Shu Y, Mattern C, Cube R, Rittle KE, McGaughey GB, Hartman GD, Tang C, Ballard J, Kuo Y, Prueksaritanont T, Nuss CE, Doran SM, Fox SV, Garson SL, Li Y, Kraus RL, Uebele VN, Renger JJ, Barrow JC. Pyridyl amides as potent inhibitors of T-type calcium channels. Bioorg Med Chem Lett 2011; 21:1692-6. [PMID: 21316226 DOI: 10.1016/j.bmcl.2011.01.089] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/19/2011] [Accepted: 01/20/2011] [Indexed: 11/18/2022]
Abstract
A novel series of amide T-type calcium channel antagonists were prepared and evaluated using in vitro and in vivo assays. Optimization of the screening hit 3 led to identification of the potent and selective T-type antagonist 37 that displayed in vivo efficacy in rodent models of epilepsy and sleep.
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Affiliation(s)
- Thomas S Reger
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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Watanuki S, Matsuura K, Tomura Y, Okada M, Okazaki T, Ohta M, Tsukamoto SI. Synthesis and Pharmacological Evaluation of 1-Isopropyl-1,2,3,4-tetrahydroisoquinoline Derivatives as Novel Antihypertensive Agents. Chem Pharm Bull (Tokyo) 2011; 59:1029-37. [DOI: 10.1248/cpb.59.1029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Design, syntheses, and SAR of 2,8-diazaspiro[4.5]decanones as T-type calcium channel antagonists. Bioorg Med Chem Lett 2010; 20:6375-8. [DOI: 10.1016/j.bmcl.2010.09.098] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 11/17/2022]
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Simões CJV, Mukherjee T, Brito RMM, Jackson RM. Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods. J Chem Inf Model 2010; 50:1806-20. [DOI: 10.1021/ci100250z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Carlos J. V. Simões
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Trishna Mukherjee
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui M. M. Brito
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Richard M. Jackson
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom and Center for Neuroscience and Cell Biology and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
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Ghemtio L, Devignes MD, Smaïl-Tabbone M, Souchet M, Leroux V, Maigret B. Comparison of three preprocessing filters efficiency in virtual screening: identification of new putative LXRbeta regulators as a test case. J Chem Inf Model 2010; 50:701-15. [PMID: 20420434 DOI: 10.1021/ci900356m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In silico screening methodologies are widely recognized as efficient approaches in early steps of drug discovery. However, in the virtual high-throughput screening (VHTS) context, where hit compounds are searched among millions of candidates, three-dimensional comparison techniques and knowledge discovery from databases should offer a better efficiency to finding novel drug leads than those of computationally expensive molecular dockings. Therefore, the present study aims at developing a filtering methodology to efficiently eliminate unsuitable compounds in VHTS process. Several filters are evaluated in this paper. The first two are structure-based and rely on either geometrical docking or pharmacophore depiction. The third filter is ligand-based and uses knowledge-based and fingerprint similarity techniques. These filtering methods were tested with the Liver X Receptor (LXR) as a target of therapeutic interest, as LXR is a key regulator in maintaining cholesterol homeostasis. The results show that the three considered filters are complementary so that their combination should generate consistent compound lists of potential hits.
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Affiliation(s)
- Léo Ghemtio
- Nancy Université, LORIA, Groupe ORPAILLEUR, Campus scientifique, BP 239, 54506 Vandoeuvre-les-Nancy Cedex, France.
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Gu SJ, Lee JK, Pae AN, Chung HJ, Rhim H, Han SY, Min SJ, Cho YS. Synthesis and biological evaluation of 1,4-diazepane derivatives as T-type calcium channel blockers. Bioorg Med Chem Lett 2010; 20:2705-8. [PMID: 20382529 DOI: 10.1016/j.bmcl.2010.03.084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 03/15/2010] [Accepted: 03/25/2010] [Indexed: 11/19/2022]
Abstract
We have synthesized and biologically evaluated 1,4-diazepane derivatives as T-type calcium channel blockers. In this study, we discovered compound 4s, a potential T-type calcium channel blocker with good selectivity over hERG and N-type calcium channels. In addition, it exhibited favorable pharmacokinetic characteristics for further investigation of T-type calcium channel related diseases.
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Affiliation(s)
- Su Jin Gu
- Life/Health Division, Korea Institute of Science and Technology, PO Box 131, Cheongyang, Seoul 130-650, Republic of Korea
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Kinnings SL, Jackson RM. LigMatch: a multiple structure-based ligand matching method for 3D virtual screening. J Chem Inf Model 2009; 49:2056-66. [PMID: 19685924 DOI: 10.1021/ci900204y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive 'template' conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping.
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Affiliation(s)
- Sarah L Kinnings
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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Jeong JA, Cho H, Jung SY, Kang HB, Park JY, Kim J, Choo DJ, Lee JY. 3D QSAR studies on 3,4-dihydroquinazolines as T-type calcium channel blocker by comparative molecular similarity indices analysis (CoMSIA). Bioorg Med Chem Lett 2009; 20:38-41. [PMID: 19951839 DOI: 10.1016/j.bmcl.2009.11.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 10/07/2009] [Accepted: 11/12/2009] [Indexed: 11/28/2022]
Abstract
A comparative molecular similarity indices analysis (CoMSIA) of a set of 42 3,4-dihydroquinazolines have been performed to find out the pharmacophore elements for T-type calcium channel blocking activity. The most potent compound, 33 (KYS05090) was used to align the molecules. As a result, we obtained 3D QSAR model which provided good predictivity for the training set (q(2)=0.642, r(2)=0.874) and the test set (r(pred)(2)=0.884). This model would guide the design of new chemical entities potentially having high potency.
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Affiliation(s)
- Jin Ah Jeong
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, Seoul 130-701, Republic of Korea
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Discovery of potent inhibitors for phosphodiesterase 5 by virtual screening and pharmacophore analysis. Acta Pharmacol Sin 2009; 30:1186-94. [PMID: 19597523 DOI: 10.1038/aps.2009.100] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
AIM To explore the potent inhibitor from one of the Traditional Chinese medicine (TCM), Epimedium sagittatum. METHODS We predicted the potent compound, ES03b, de novo evolution from the four Epimedium sagittatum components were verified by molecular docking, pharmacophore analysis, and analysis of quantitative structure-activity relationship (QSAR) model, which was constructed by multiple linear regression. RESULTS ES03b was chosen to undergo drug modification via de novo evolution. By analyzing the pharmacophore features, we found that the hydrophobic core in the binding site and the hydrogen bond generated at Asn663 played key roles in designing PDE5 inhibitors. ES03b generated 49 diversities (Evo01-49). Evo48 had high activity in prediction. Although the value of prediction was overestimated, Evo48 was suggested as the potent lead. CONCLUSION In this study, we showed that the hydrophobic core in the binding site and hydrogen bond production on Asn663 played key roles to design PDE5 inhibitors. From several require validation analysis, Evo48 was suggested to be a potent inhibitor.
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Uebele VN, Nuss CE, Fox SV, Garson SL, Cristescu R, Doran SM, Kraus RL, Santarelli VP, Li Y, Barrow JC, Yang ZQ, Schlegel KAS, Rittle KE, Reger TS, Bednar RA, Lemaire W, Mullen FA, Ballard JE, Tang C, Dai G, McManus OB, Koblan KS, Renger JJ. Positive Allosteric Interaction of Structurally Diverse T-Type Calcium Channel Antagonists. Cell Biochem Biophys 2009; 55:81-93. [DOI: 10.1007/s12013-009-9057-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 06/23/2009] [Indexed: 01/16/2023]
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Huc S, Monteil A, Bidaud I, Barbara G, Chemin J, Lory P. Regulation of T-type calcium channels: Signalling pathways and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:947-52. [DOI: 10.1016/j.bbamcr.2008.11.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 11/04/2008] [Accepted: 11/06/2008] [Indexed: 11/15/2022]
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Lead Discovery Using Virtual Screening. TOPICS IN MEDICINAL CHEMISTRY 2009. [PMCID: PMC7176223 DOI: 10.1007/7355_2009_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The practice of virtual screening (VS) to identify chemical leads to known or novel targets is becoming a core function of the computational chemist within industry. By employing a range of techniques, when attempting to identify compounds with activity against a biological target, a small focused subset of a larger collection of compounds can be identified and tested, often with results much better than selecting a similar number of compounds at random. We will review the key methods available, their relative success, and provide practical insights into best practices and key gaps. We will also argue that the capability of VS methods has grown to a point where fuller integration with experimental methods, including HTS, could increase the effectiveness of both.
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Childers WE, Gilbert AM, Kennedy JD, Whiteside GT. Advances in the development of novel analgesics. Expert Opin Ther Pat 2008. [DOI: 10.1517/13543776.18.9.1027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Synthesis and evaluation of α,α′-disubstituted phenylacetate derivatives for T-type calcium channel blockers. Bioorg Med Chem Lett 2008; 18:4424-7. [DOI: 10.1016/j.bmcl.2008.06.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/04/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
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Seo HN, Choi JY, Choe YJ, Kim Y, Rhim H, Lee SH, Kim J, Joo DJ, Lee JY. Discovery of potent T-type calcium channel blocker. Bioorg Med Chem Lett 2007; 17:5740-3. [PMID: 17869104 DOI: 10.1016/j.bmcl.2007.08.070] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/16/2007] [Accepted: 08/29/2007] [Indexed: 11/26/2022]
Abstract
The intensive SAR study of 3,4-dihydroquinazoline series led to the most potent compound 10 (KYS05090: IC(50)=41+/-1 nM) against T-type calcium channel and its potency is nearly comparable to that of Kurtoxin. As a small organic molecule, this compound showed the highest blocking activity reported to date.
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Affiliation(s)
- Han Na Seo
- Research Institute for Basic Sciences and Department of Chemistry, Kyung Hee University, Seoul 130-701, Republic of Korea
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Abstract
Despite their presence in many tissues and their potential implication in various disease states, low-voltage activated T-type calcium channels (T-channels) have only recently become targets of interest. Unfortunately, the lack of selective T-channel blockers has hampered further characterisation of these channels. The recent availability of cloned T-channels, the Ca(V)3 proteins, facilitates identification of novel T-channel blockers. Also, studies performed in knockout animals have fostered novel interest. Selective inhibition of T-channels may have clinical importance in cardiovascular diseases, some forms of epilepsy, sleep disorders, pain and possibly cancer. This review focuses on novel research approaches to discover potent and selective T-channel modulators. These molecules may be potential drugs for treating human diseases, as well as important tools to decipher the physiological role of these channels.
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Affiliation(s)
- Philippe Lory
- Institut de Génomique Fonctionnelle, Département de Physiologie, CNRS UMR 5203, INSERM U661, IFR3, Universités de Montpellier I and II, Montpellier cedex 05, France.
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Sperandio O, Andrieu O, Miteva MA, Vo MQ, Souaille M, Delfaud F, Villoutreix BO. MED-SuMoLig: A New Ligand-Based Screening Tool for Efficient Scaffold Hopping. J Chem Inf Model 2007; 47:1097-110. [PMID: 17477521 DOI: 10.1021/ci700031v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification of small molecules with selective bioactivity, whether intended as potential therapeutics or as tools for experimental research, is central to progress in medicine and in the life sciences. To facilitate such study, we have developed a ligand-based program well-suited for effective screening of large compound collections. This package, MED-SuMoLig, combines a SMARTS-driven substructure search aiming at 3D pharmacophore profiling and computation of the local atomic density of the compared molecules. The screening utility was then investigated using 52 diverse active molecules (against CDK2, Factor Xa, HIV-1 protease, neuraminidase, ribonuclease A, and thymidine kinase) merged to a library of about 40,000 putative inactive (druglike) compounds. In all cases, the program recovered more than half of the actives in the top 3% of the screened library. We also compared the performance of MED-SuMoLig with that of ChemMine or of ROCS and found that MED-SuMoLig outperformed both methods for CDK2 and Factor Xa in terms of enrichment rates or performed equally well for the other targets.
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Affiliation(s)
- Olivier Sperandio
- INSERM U648, University Paris V, 45 rue des Sts peres, 75006 Paris, France
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