1
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Brust CA, Swanson MA, Bohn LM. Structural and functional insights into the G protein-coupled receptors: CB1 and CB2. Biochem Soc Trans 2023; 51:1533-1543. [PMID: 37646476 PMCID: PMC10586759 DOI: 10.1042/bst20221316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023]
Abstract
The cannabinoid receptors CB1 and CB2 mediate a variety of physiological processes and continue to be explored as desirable drug targets. Both receptors are activated by the endogenous endocannabinoids and the psychoactive components of marijuana. Over the years, many efforts have been made to make selective ligands; however, the high degree of homology between cannabinoid receptor subtypes introduces challenges in studying either receptor in isolation. Recent advancements in structure biology have resulted in a surge of high-resolution structures, enriching our knowledge and understanding of receptor structure and function. In this review, of recent cannabinoid receptor structures, key features of the inactive and active state CB1 and CB2 are presented. These structures will provide additional insight into the modulation and signaling mechanism of cannabinoid receptors CB1 and CB2 and aid in the development of future therapeutics.
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Affiliation(s)
- Christina A. Brust
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
| | - Matthew A. Swanson
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
| | - Laura M. Bohn
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL 33458, U.S.A
- The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, La Jolla, CA 92037, U.S.A
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2
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Hosami F, Salimi V, Safizadeh B, Abedini A, Ghadimkhah MH, Tavakoli-Yaraki M. Evaluation of the local and circulating expression level of cannabinoid receptor 2 in patients with lung cancer. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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Maqbool M, Gadhavi J, Singh A, Hivare P, Gupta S, Hoda N. Unravelling the potency of triazole analogues for inhibiting α-synuclein fibrillogenesis and in vitro disaggregation. Org Biomol Chem 2021; 19:1589-1603. [PMID: 33527970 DOI: 10.1039/d0ob02226h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A series of triazole-based compounds was synthesized using a click chemistry approach and evaluated for the inhibition of α-synuclein (α-syn) fibrillogenesis and its disaggregation. Compounds Tr3, Tr7, Tr12, Tr15, and Tr16 exhibited good effect in inhibiting α-syn fibrillogenesis confirmed by Thioflavin-T assay and fluorescence microscopy and α-syn disaggregation confirmed by fluorescence microscopy. Molecular docking was used to understand the plausible mechanism of the test compounds for inhibiting the α-syn fibrillogenesis and to verify the in vitro results. Compounds Tr3, Tr7, Tr12, Tr15 and Tr16 showed good binding interactions with the essential amino acid residues of α-syn. The compounds which were found to be good inhibitors or disaggregators had no toxic effects on the SH-SY5Y cell line. These compounds have the potential to be developed as therapeutic interventions against synucleinopathies including Parkinson's disease and Lewy body dementia.
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Affiliation(s)
- Mudasir Maqbool
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
| | - Joshna Gadhavi
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Anju Singh
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
| | - Pravin Hivare
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Sharad Gupta
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Lab., Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.
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4
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Zondagh LS, Malan SF, Joubert J. Design, synthesis and biological evaluation of edaravone derivatives bearing the N-benzyl pyridinium moiety as multifunctional anti-Alzheimer's agents. J Enzyme Inhib Med Chem 2020; 35:1596-1605. [PMID: 32779503 PMCID: PMC7470113 DOI: 10.1080/14756366.2020.1801673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 12/31/2022] Open
Abstract
A series of multi-target directed edaravone derivatives bearing N-benzyl pyridinium moieties were designed and synthesised. Edaravone is a potent antioxidant with significant neuroprotective effects and N-benzyl pyridinium has previously exhibited positive results as part of a dual-site binding, peripheral anionic site (PAS) and catalytic anionic site (CAS), acetylcholinesterase (AChE) inhibitor. The designed edaravone-N-benzyl pyridinium hybrid compounds were docked within the AChE active site. The results indicated interactions with conserved amino acids (Trp279 in PAS and Trp84 in CAS), suggesting good dual-site inhibitory activity. Significant in vitro AChE inhibitory activities were observed for selected compounds (IC50: 1.2-4.6 µM) with limited butyrylcholinesterase inhibitory activity (IC50's >160 µM), indicating excellent selectivity towards AChE (SI: 46 - >278). The compounds also showed considerable antioxidant ability, similar to edaravone. In silico studies indicated that these compounds should cross the blood-brain barrier, making them promising lead molecules in the development of anti-Alzheimer's agents.
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Affiliation(s)
- Luke S. Zondagh
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Bellville, South Africa
| | - Sarel F. Malan
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Bellville, South Africa
| | - Jacques Joubert
- Pharmaceutical Chemistry, School of Pharmacy, University of the Western Cape, Bellville, South Africa
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5
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Haspula D, Clark MA. Cannabinoid Receptors: An Update on Cell Signaling, Pathophysiological Roles and Therapeutic Opportunities in Neurological, Cardiovascular, and Inflammatory Diseases. Int J Mol Sci 2020; 21:E7693. [PMID: 33080916 PMCID: PMC7590033 DOI: 10.3390/ijms21207693] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022] Open
Abstract
The identification of the human cannabinoid receptors and their roles in health and disease, has been one of the most significant biochemical and pharmacological advancements to have occurred in the past few decades. In spite of the major strides made in furthering endocannabinoid research, therapeutic exploitation of the endocannabinoid system has often been a challenging task. An impaired endocannabinoid tone often manifests as changes in expression and/or functions of type 1 and/or type 2 cannabinoid receptors. It becomes important to understand how alterations in cannabinoid receptor cellular signaling can lead to disruptions in major physiological and biological functions, as they are often associated with the pathogenesis of several neurological, cardiovascular, metabolic, and inflammatory diseases. This review focusses mostly on the pathophysiological roles of type 1 and type 2 cannabinoid receptors, and it attempts to integrate both cellular and physiological functions of the cannabinoid receptors. Apart from an updated review of pre-clinical and clinical studies, the adequacy/inadequacy of cannabinoid-based therapeutics in various pathological conditions is also highlighted. Finally, alternative strategies to modulate endocannabinoid tone, and future directions are also emphasized.
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Affiliation(s)
- Dhanush Haspula
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA;
| | - Michelle A. Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
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6
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Ji B, Liu S, He X, Man VH, Xie XQ, Wang J. Prediction of the Binding Affinities and Selectivity for CB1 and CB2 Ligands Using Homology Modeling, Molecular Docking, Molecular Dynamics Simulations, and MM-PBSA Binding Free Energy Calculations. ACS Chem Neurosci 2020; 11:1139-1158. [PMID: 32196303 DOI: 10.1021/acschemneuro.9b00696] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Cannabinoids are a group of chemical compounds that have been used for thousands of years due to their psychoactive function and systemic physiological effects. There are at least two types of cannabinoid receptors, CB1 and CB2, which belong to the G protein-coupled receptor superfamily and can trigger different signaling pathways to exert their physiological functions. In this study, several representative agonists and antagonists of both CB1 and CB2 were systematically studied to predict their binding affinities and selectivity against both cannabinoid receptors using a set of hierarchical molecular modeling and simulation techniques, including homology modeling, molecular docking, molecular dynamics (MD) simulations and end point binding free energy calculations using the molecular mechanics/Poisson-Boltzmann surface area-WSAS (MM-PBSA-WSAS) method, and molecular mechanics/generalized Born surface area (MM-GBSA) free energy decomposition. Encouragingly, the calculated binding free energies correlated very well with the experimental values and the correlation coefficient square (R2), 0.60, was much higher than that of an efficient but less accurate docking scoring function (R2 = 0.37). The hotspot residues for CB1 and CB2 in both active and inactive conformations were identified via MM-GBSA free energy decomposition analysis. The comparisons of binding free energies, ligand-receptor interaction patterns, and hotspot residues among the four systems, namely, agonist-bound CB1, agonist-bound CB2, antagonist-bound CB1, and antagonist-bound CB2, enabled us to investigate and identify distinct binding features of these four systems, with which one can rationally design potent, selective, and function-specific modulators for the cannabinoid receptors.
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Affiliation(s)
- Beihong Ji
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Shuhan Liu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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7
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Ye L, Cao Z, Wang W, Zhou N. New Insights in Cannabinoid Receptor Structure and Signaling. Curr Mol Pharmacol 2020; 12:239-248. [PMID: 30767756 DOI: 10.2174/1874467212666190215112036] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Cannabinoid has long been used for medicinal purposes. Cannabinoid signaling has been considered the therapeutic target for treating pain, addiction, obesity, inflammation, and other diseases. Recent studies have suggested that in addition to CB1 and CB2, there are non-CB1 and non-CB2 cannabinoid-related orphan GPCRs including GPR18, GPR55, and GPR119. In addition, CB1 and CB2 display allosteric binding and biased signaling, revealing correlations between biased signaling and functional outcomes. Interestingly, new investigations have indicated that CB1 is functionally present within the mitochondria of striated and heart muscles directly regulating intramitochondrial signaling and respiration. CONCLUSION In this review, we summarize the recent progress in cannabinoid-related orphan GPCRs, CB1/CB2 structure, Gi/Gs coupling, allosteric ligands and biased signaling, and mitochondria-localized CB1, and discuss the future promise of this research.
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Affiliation(s)
- Lingyan Ye
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Zheng Cao
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Weiwei Wang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Naiming Zhou
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
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8
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Journigan VB, Feng Z, Rahman S, Wang Y, Amin ARMR, Heffner CE, Bachtel N, Wang S, Gonzalez-Rodriguez S, Fernández-Carvajal A, Fernández-Ballester G, Hilton JK, Van Horn WD, Ferrer-Montiel A, Xie XQ, Rahman T. Structure-Based Design of Novel Biphenyl Amide Antagonists of Human Transient Receptor Potential Cation Channel Subfamily M Member 8 Channels with Potential Implications in the Treatment of Sensory Neuropathies. ACS Chem Neurosci 2020; 11:268-290. [PMID: 31850745 DOI: 10.1021/acschemneuro.9b00404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Structure-activity relationship studies of a reported menthol-based transient receptor potential cation channel subfamily M member 8 channel (TRPM8) antagonist, guided by computational simulations and structure-based design, uncovers a novel series of TRPM8 antagonists with >10-fold selectivity versus related TRP subtypes. Spiro[4.5]decan-8-yl analogue 14 inhibits icilin-evoked Ca2+ entry in HEK-293 cells stably expressing human TRPM8 (hTRPM8) with an IC50 of 2.4 ± 1.0 nM, while in whole-cell patch-clamp recordings this analogue inhibits menthol-evoked currents with a hTRPM8 IC50 of 64 ± 2 nM. Molecular dynamics (MD) simulations of compound 14 in our homology model of hTRPM8 suggest that this antagonist forms extensive hydrophobic contacts within the orthosteric site. In the wet dog shakes (WDS) assay, compound 14 dose-dependently blocks icilin-triggered shaking behaviors in mice. Upon local administration, compound 14 dose dependently inhibits cold allodynia evoked by the chemotherapy oxaliplatin in a murine model of peripheral neuropathy at microgram doses. Our findings suggest that 14 and other biphenyl amide analogues within our series can find utility as potent antagonist chemical probes derived from (-)-menthol as well as small molecule therapeutic scaffolds for chemotherapy-induced peripheral neuropathy (CIPN) and other sensory neuropathies.
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Affiliation(s)
- V. Blair Journigan
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia 25755, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Saifur Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1TN, United Kingdom
| | - Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - A. R. M. Ruhul Amin
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia 25755, United States
| | - Colleen E. Heffner
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
| | - Nicholas Bachtel
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Sara Gonzalez-Rodriguez
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Asia Fernández-Carvajal
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Gregorio Fernández-Ballester
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Jacob K. Hilton
- The School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- the Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- The Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287, United States
| | - Wade D. Van Horn
- The School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- the Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- The Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287, United States
| | - Antonio Ferrer-Montiel
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1TN, United Kingdom
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9
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Kallinen A, Boyd R, Lane S, Bhalla R, Mardon K, Stimson DHR, Werry EL, Fulton R, Connor M, Kassiou M. Synthesis and in vitro evaluation of fluorine-18 benzimidazole sulfones as CB2 PET-radioligands. Org Biomol Chem 2019; 17:5086-5098. [PMID: 31070218 DOI: 10.1039/c9ob00656g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cannabinoid type 2 receptor (CB2) is up-regulated on activated microglial cells and can potentially be used as a biomarker for PET-imaging of neuroinflammation. In this study the synthesis and pharmacological evaluation of novel fluorinated pyridyl and ethyl sulfone analogues of 2-(tert-butyl)-5-((2-fluoropyridin-4-yl)sulfonyl)-1-(2-methylpentyl)-1H-benzo[d]imidazole (rac-1a) are described. In general, the ligands showed low nanomolar potency (CB2 EC50 < 10 nM) and excellent selectivity over the CB1 subtype (>10 000×). Selected ligands 1d, 1e, 1g and 3l showing high CB2 binding affinity (Ki < 10 nM) were radiolabelled with fluorine-18 from chloropyridyl and alkyl tosylate precursors with good to high isolated radioactive yields (25-44%, non-decay corrected, at the end of synthesis). CB2-specific binding of the radioligand candidates [18F]-1d and [18F]-3l was assessed on rat spleen cryosections using in vitro autoradiography. The results warrant further in vivo evaluation of the tracer candidates as prospective CB2 PET-imaging agents.
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Affiliation(s)
- Annukka Kallinen
- School of Chemistry, The University of Sydney, NSW 2006, Australia.
| | - Rochelle Boyd
- Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - Samuel Lane
- Faculty of Health Sciences, The University of Sydney, NSW 2050, Australia
| | - Rajiv Bhalla
- The Centre for Advanced Imaging, The University of Queensland, QLD 4072, Australia
| | - Karine Mardon
- The Centre for Advanced Imaging, The University of Queensland, QLD 4072, Australia
| | - Damion H R Stimson
- The Centre for Advanced Imaging, The University of Queensland, QLD 4072, Australia
| | - Eryn L Werry
- School of Chemistry, The University of Sydney, NSW 2006, Australia.
| | - Roger Fulton
- Faculty of Health Sciences, The University of Sydney, NSW 2050, Australia
| | - Mark Connor
- Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - Michael Kassiou
- School of Chemistry, The University of Sydney, NSW 2006, Australia.
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10
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Wu N, Feng Z, He X, Kwon W, Wang J, Xie XQ. Insight of Captagon Abuse by Chemogenomics Knowledgebase-guided Systems Pharmacology Target Mapping Analyses. Sci Rep 2019; 9:2268. [PMID: 30783122 PMCID: PMC6381188 DOI: 10.1038/s41598-018-35449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022] Open
Abstract
Captagon, known by its genetic name Fenethylline, is an addictive drug that complicates the War on Drugs. Captagon has a strong CNS stimulating effect than its primary metabolite, Amphetamine. However, multi-targets issues associated with the drug and metabolites as well as its underlying mechanisms have not been fully defined. In the present work, we applied our established drug-abuse chemogenomics-knowledgebase systems pharmacology approach to conduct targets/off-targets mapping (SP-Targets) investigation of Captagon and its metabolites for hallucination addiction, and also analyzed the cell signaling pathways for both Amphetamine and Theophylline with data mining of available literature. Of note, Amphetamine, an agonist for trace amine-associated receptor 1 (TAAR1) with enhancing dopamine signaling (increase of irritability, aggression, etc.), is the main cause of Captagon addiction; Theophylline, an antagonist that blocks adenosine receptors (e.g. A2aR) in the brain responsible for restlessness and painlessness, may attenuate the behavioral sensitization caused by Amphetamine. We uncovered that Theophylline's metabolism and elimination could be retarded due to competition and/or blockage of the CYP2D6 enzyme by Amphetamine; We also found that the synergies between these two metabolites cause Captagon's psychoactive effects to act faster and far more potently than those of Amphetamine alone. We carried out further molecular docking modeling and molecular dynamics simulation to explore the molecular interactions between Amphetamine and Theophylline and their important GPCRs targets, including TAAR1 and adenosine receptors. All of the systems pharmacology analyses and results will shed light insight into a better understanding of Captagon addiction and future drug abuse prevention.
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Affiliation(s)
- Nan Wu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
| | - William Kwon
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States.
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11
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Pandey P, Roy KK, Doerksen RJ. Negative allosteric modulators of cannabinoid receptor 2: protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist. J Biomol Struct Dyn 2019; 38:32-47. [PMID: 30652534 DOI: 10.1080/07391102.2019.1567384] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Selective activation of the cannabinoid receptor subtype 2 (CB2) shows promise for treating pain, inflammation, multiple sclerosis, cancer, ischemic/reperfusion injury and osteoporosis. Target selectivity and off-target side effects are two major limiting factors for orthosteric ligands, and therefore, the search for allosteric modulators (AMs) is a widely used drug discovery approach. To date, only a limited number of negative CB2 AMs have been identified, possessing only micromolar activity at best, and the CB2 receptor's allosteric site(s) are not well characterized. Herein, we used computational approaches including receptor modeling, site mapping, docking, molecular dynamics (MD) simulations and binding free energy calculations to predict, characterize and validate allosteric sites within the complex of the CB2 receptor with bound orthosteric agonist CP55,940. After docking of known negative CB2 allosteric modulators (NAMs), dihydro-gambogic acid (DHGA) and trans-β-caryophyllene (TBC) (note that TBC also shows agonist activity), at the predicted allosteric sites, the best total complex with CB2, CP55,940 and NAM was embedded into a hydrated lipid bilayer and subjected to a 200 ns MD simulation. The presence of an AM affected the CB2-CP55,940 complex, altering the relative positioning of the toggle switch residues and promoting a strong π-π interaction between Phe1173.36 and Trp2586.48. Binding of either TBC or DHGA to a putative allosteric pocket directly adjacent to the orthosteric ligand reduced the binding free energy of CP55,940, which is consistent with the expected effect of a negative AM. The identified allosteric sites present immense scope for the discovery of novel classes of CB2 AMs.
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Affiliation(s)
- Pankaj Pandey
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, The University of Mississippi, University, MS, USA
| | - Kuldeep K Roy
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, The University of Mississippi, University, MS, USA.,National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, India
| | - Robert J Doerksen
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, The University of Mississippi, University, MS, USA.,Research Institute of Pharmaceutical Sciences, School of Pharmacy, The University of Mississippi, University, MS, USA
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12
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Study of cannabinoid receptor 2 Q63R gene polymorphism in Lebanese patients with rheumatoid arthritis. Clin Rheumatol 2018; 37:2933-2938. [DOI: 10.1007/s10067-018-4217-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 10/28/2022]
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13
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Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 2018; 113:2634-2649. [PMID: 29262358 DOI: 10.1016/j.bpj.2017.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022] Open
Abstract
As a protease complex involved in the cleavage of amyloid precursor proteins that lead to the formation of amyloid β fibrils implicated in Alzheimer's disease, γ-secretase is an important target for developing therapeutics against Alzheimer's disease. γ-secretase is composed of four subunits: nicastrin (NCT) in the extracellular (EC) domain, presenilin-1 (PS1), anterior pharynx defective 1, and presenilin enhancer 2 in the transmembrane (TM) domain. NCT and PS1 play important roles in binding amyloid β precursor proteins and modulating PS1 catalytic activity. Yet, the molecular mechanisms of coupling between substrate/modulator binding and catalytic activity remain to be elucidated. Recent determination of intact human γ-secretase cryo-electron microscopy structure has opened the way for a detailed investigation of the structural dynamics of this complex. Our analysis, based on a membrane-coupled anisotropic network model, reveals two types of NCT motions, bending and twisting, with respect to PS1. These underlie the fluctuations between the "open" and "closed" states of the lid-like NCT with respect to a hydrophilic loop 1 (HL1) on PS1, thus allowing or blocking access of the substrate peptide (EC portion) to HL1 and to the neighboring helix TM2. In addition to this alternating access mechanism, fluctuations in the volume of the PS1 central cavity facilitate the exposure of the catalytic site for substrate cleavage. Druggability simulations show that γ-secretase presents several hot spots for either orthosteric or allosteric inhibition of catalytic activity, consistent with experimental data. In particular, a hinge region at the interface between the EC and TM domains, near the interlobe groove of NCT, emerges as an allo-targeting site that would impact the coupling between HL1/TM2 and the catalytic pocket, opening, to our knowledge, new avenues for structure-based design of novel allosteric modulators of γ-secretase protease activity.
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p62/SQSTM1/Sequestosome-1 is an N-recognin of the N-end rule pathway which modulates autophagosome biogenesis. Nat Commun 2017; 8:102. [PMID: 28740232 PMCID: PMC5524641 DOI: 10.1038/s41467-017-00085-7] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/01/2017] [Indexed: 11/09/2022] Open
Abstract
Macroautophagy mediates the selective degradation of proteins and non-proteinaceous cellular constituents. Here, we show that the N-end rule pathway modulates macroautophagy. In this mechanism, the autophagic adapter p62/SQSTM1/Sequestosome-1 is an N-recognin that binds type-1 and type-2 N-terminal degrons (N-degrons), including arginine (Nt-Arg). Both types of N-degrons bind its ZZ domain. By employing three-dimensional modeling, we developed synthetic ligands to p62 ZZ domain. The binding of Nt-Arg and synthetic ligands to ZZ domain facilitates disulfide bond-linked aggregation of p62 and p62 interaction with LC3, leading to the delivery of p62 and its cargoes to the autophagosome. Upon binding to its ligand, p62 acts as a modulator of macroautophagy, inducing autophagosome biogenesis. Through these dual functions, cells can activate p62 and induce selective autophagy upon the accumulation of autophagic cargoes. We also propose that p62 mediates the crosstalk between the ubiquitin-proteasome system and autophagy through its binding Nt-Arg and other N-degrons.Soluble misfolded proteins that fail to be degraded by the ubiquitin proteasome system (UPS) are redirected to autophagy via specific adaptors, such as p62. Here the authors show that p62 recognises N-degrons in these proteins, acting as a N-recognin from the proteolytic N-end rule pathway, and targets these cargos to autophagosomal degradation.
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Abstract
The CB1 and CB2 cannabinoid receptors (CB1R, CB2R) are members of the G protein-coupled receptor (GPCR) family that were identified over 20 years ago. CB1Rs and CB2Rs mediate the effects of Δ9-tetrahydrocannabinol (Δ9-THC), the principal psychoactive constituent of marijuana, and subsequently identified endogenous cannabinoids (endocannabinoids) anandamide and 2-arachidonoyl glycerol. CB1Rs and CB2Rs have both similarities and differences in their pharmacology. Both receptors recognize multiple classes of agonist and antagonist compounds and produce an array of distinct downstream effects. Natural polymorphisms and alternative splice variants may also contribute to their pharmacological diversity. As our knowledge of the distinct differences grows, we may be able to target select receptor conformations and their corresponding pharmacological responses. This chapter will discuss their pharmacological characterization, distribution, phylogeny, and signaling pathways. In addition, the effects of extended agonist exposure and how that affects signaling and expression patterns of the receptors are considered.
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MESH Headings
- Alternative Splicing/genetics
- Animals
- Humans
- Phylogeny
- Polymorphism, Genetic
- Receptor, Cannabinoid, CB1/agonists
- Receptor, Cannabinoid, CB1/genetics
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB2/agonists
- Receptor, Cannabinoid, CB2/genetics
- Receptor, Cannabinoid, CB2/metabolism
- Signal Transduction/drug effects
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Affiliation(s)
- Allyn C Howlett
- Center for Research on Substance Use and Addiction, Wake Forest University Health Sciences, Winston-Salem, NC, United States
| | - Mary E Abood
- Center for Substance Abuse Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States.
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16
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Chen S, Feng Z, Wang Y, Ma S, Hu Z, Yang P, Chai Y, Xie X. Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. J Chem Inf Model 2017; 57:1101-1111. [PMID: 28422491 PMCID: PMC6732210 DOI: 10.1021/acs.jcim.6b00672] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tumor necrosis factor α (TNF-α) is overexpressed in various diseases, and it has been a validated therapeutic target for autoimmune diseases. All therapeutics currently used to target TNF-α are biomacromolecules, and limited numbers of TNF-α chemical inhibitors have been reported, which makes the identification of small-molecule alternatives an urgent need. Recent studies have mainly focused on identifying small molecules that directly bind to TNF-α or TNF receptor-1 (TNFR1), inhibit the interaction between TNF-α and TNFR1, and/or regulate related signaling pathways. In this study, we combined in silico methods with biophysical and cell-based assays to identify novel antagonists that bind to TNF-α or TNFR1. Pharmacophore model filtering and molecular docking were applied to identify potential TNF-α antagonists. In regard to TNFR1, we constructed a three-dimensional model of the TNF-α-TNFR1 complex and carried out molecular dynamics simulations to sample the conformations. The residues in TNF-α that have been reported to play important roles in the TNF-α-TNFR1 complex were removed to form a pocket for further virtual screening of TNFR1-binding ligands. We obtained 20 virtual hits and tested them using surface plasmon resonance-based assays, which resulted in one ligand that binds to TNFR1 and four ligands with different scaffolds that bind to TNF-α. T1 and R1, the two most active compounds with Kd values of 11 and 16 μM for TNF-α and TNFR1, respectively, showed activities similar to those of known antagonists. Further cell-based assays also demonstrated that T1 and R1 have similar activities compared to the known TNF-α antagonist C87. Our work has not only produced several TNF-α and TNFR1 antagonists with novel scaffolds for further structural optimization but also showcases the power of our in silico methods for TNF-α- and TNFR1-based drug discovery.
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Affiliation(s)
- Si Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yun Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ziheng Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Xiangqun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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17
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Kho DT, Glass M, Graham ES. Is the Cannabinoid CB 2 Receptor a Major Regulator of the Neuroinflammatory Axis of the Neurovascular Unit in Humans? CANNABINOID PHARMACOLOGY 2017; 80:367-396. [DOI: 10.1016/bs.apha.2017.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Xu X, Ma S, Feng Z, Hu G, Wang L, Xie XQ. Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. J Mol Graph Model 2016; 70:284-295. [PMID: 27810775 PMCID: PMC5327504 DOI: 10.1016/j.jmgm.2016.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/18/2016] [Accepted: 08/06/2016] [Indexed: 01/22/2023]
Abstract
Drug abuse is a serious problem worldwide. Recently, hallucinogens have been reported as a potential preventative and auxiliary therapy for substance abuse. However, the use of hallucinogens as a drug abuse treatment has potential risks, as the fundamental mechanisms of hallucinogens are not clear. So far, no scientific database is available for the mechanism research of hallucinogens. We constructed a hallucinogen-specific chemogenomics database by collecting chemicals, protein targets and pathways closely related to hallucinogens. This information, together with our established computational chemogenomics tools, such as TargetHunter and HTDocking, provided a one-step solution for the mechanism study of hallucinogens. We chose salvinorin A, a potent hallucinogen extracted from the plant Salvia divinorum, as an example to demonstrate the usability of our platform. With the help of HTDocking program, we predicted four novel targets for salvinorin A, including muscarinic acetylcholine receptor 2, cannabinoid receptor 1, cannabinoid receptor 2 and dopamine receptor 2. We looked into the interactions between salvinorin A and the predicted targets. The binding modes, pose and docking scores indicate that salvinorin A may interact with some of these predicted targets. Overall, our database enriched the information of systems pharmacological analysis, target identification and drug discovery for hallucinogens.
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Affiliation(s)
- Xiaomeng Xu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Guanxing Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Zhang Y, Wang L, Feng Z, Cheng H, McGuire TF, Ding Y, Cheng T, Gao Y, Xie XQ. StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. J Chem Inf Model 2016; 56:1995-2004. [PMID: 27643925 DOI: 10.1021/acs.jcim.5b00748] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Given the capacity of self-renewal and multilineage differentiation, stem cells are promising sources for use in regenerative medicines as well as in the clinical treatment of certain hematological malignancies and degenerative diseases. Complex networks of cellular signaling pathways largely determine stem cell fate and function. Small molecules that modulate these pathways can provide important biological and pharmacological insights. However, it is still challenging to identify the specific protein targets of these compounds, to explore the changes in stem cell phenotypes induced by compound treatment and to ascertain compound mechanisms of action. To facilitate stem cell related small molecule study and provide a better understanding of the associated signaling pathways, we have constructed a comprehensive domain-specific chemogenomics resource, called StemCellCKB ( http://www.cbligand.org/StemCellCKB/ ). This new cloud-computing platform describes the chemical molecules, genes, proteins, and signaling pathways implicated in stem cell regulation. StemCellCKB is also implemented with web applications designed specifically to aid in the identification of stem cell relevant protein targets, including TargetHunter, a machine-learning algorithm for predicting small molecule targets based on molecular fingerprints, and HTDocking, a high-throughput docking module for target prediction and systems-pharmacology analyses. We have systematically tested StemCellCKB to verify data integrity. Target-prediction accuracy has also been validated against the reported known target/compound associations. This proof-of-concept example demonstrates that StemCellCKB can (1) accurately predict the macromolecular targets of existing stem cell modulators and (2) identify novel small molecules capable of probing stem cell signaling mechanisms, for use in systems-pharmacology studies. StemCellCKB facilitates the exploration and exchange of stem cell chemogenomics data among members of the broader research community.
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Affiliation(s)
- Yu Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States.,Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Tianjin 300020, P. R. China
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Haizi Cheng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Terence Francis McGuire
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Yahui Ding
- Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Tianjin 300020, P. R. China
| | - Tao Cheng
- Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Tianjin 300020, P. R. China
| | - Yingdai Gao
- Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College , Tianjin 300020, P. R. China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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20
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Zhang H, Ma S, Feng Z, Wang D, Li C, Cao Y, Chen X, Liu A, Zhu Z, Zhang J, Zhang G, Chai Y, Wang L, Xie XQ. Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula. Sci Rep 2016; 6:33963. [PMID: 27678063 PMCID: PMC5039409 DOI: 10.1038/srep33963] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022] Open
Abstract
Combination therapy is a popular treatment for various diseases in the clinic. Among the successful cases, Traditional Chinese Medicinal (TCM) formulae can achieve synergistic effects in therapeutics and antagonistic effects in toxicity. However, characterizing the underlying molecular synergisms for the combination of drugs remains a challenging task due to high experimental expenses and complication of multicomponent herbal medicines. To understand the rationale of combination therapy, we investigated Sini Decoction, a well-known TCM consisting of three herbs, as a model. We applied our established diseases-specific chemogenomics databases and our systems pharmacology approach TargetHunter to explore synergistic mechanisms of Sini Decoction in the treatment of cardiovascular diseases. (1) We constructed a cardiovascular diseases-specific chemogenomics database, including drugs, target proteins, chemicals, and associated pathways. (2) Using our implemented chemoinformatics tools, we mapped out the interaction networks between active ingredients of Sini Decoction and their targets. (3) We also in silico predicted and experimentally confirmed that the side effects can be alleviated by the combination of the components. Overall, our results demonstrated that our cardiovascular disease-specific database was successfully applied for systems pharmacology analysis of a complicated herbal formula in predicting molecular synergetic mechanisms, and led to better understanding of a combinational therapy.
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Affiliation(s)
- Hai Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Dongyao Wang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Chengjian Li
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yan Cao
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Xiaofei Chen
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Aijun Liu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Zhenyu Zhu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Junping Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Guoqing Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yifeng Chai
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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21
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Hu J, Feng Z, Ma S, Zhang Y, Tong Q, Alqarni MH, Gou X, Xie XQ. Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery. J Chem Inf Model 2016; 56:1152-63. [PMID: 27186994 PMCID: PMC5395206 DOI: 10.1021/acs.jcim.5b00739] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cannabinoid receptor 2 (CB2), a G protein-coupled receptor (GPCR), is a promising target for the treatment of neuropathic pain, osteoporosis, immune system, cancer, and drug abuse. The lack of an experimental three-dimensional CB2 structure has hindered not only the development of studies of conformational differences between the inactive and active CB2 but also the rational discovery of novel functional compounds targeting CB2. In this work, we constructed models of both inactive and active CB2 by homology modeling. Then we conducted two comparative 100 ns molecular dynamics (MD) simulations on the two systems-the active CB2 bound with both the agonist and G protein and the inactive CB2 bound with inverse agonist-to analyze the conformational difference of CB2 proteins and the key residues involved in molecular recognition. Our results showed that the inactive CB2 and the inverse agonist remained stable during the MD simulation. However, during the MD simulations, we observed dynamical details about the breakdown of the "ionic lock" between R131(3.50) and D240(6.30) as well as the outward/inward movements of transmembrane domains of the active CB2 that bind with G proteins and agonist (TM5, TM6, and TM7). All of these results are congruent with the experimental data and recent reports. Moreover, our results indicate that W258(6.48) in TM6 and residues in TM4 (V164(4.56)-L169(4.61)) contribute greatly to the binding of the agonist on the basis of the binding energy decomposition, while residues S180-F183 in extracellular loop 2 (ECL2) may be of importance in recognition of the inverse agonist. Furthermore, pharmacophore modeling and virtual screening were carried out for the inactive and active CB2 models in parallel. Among all 10 hits, two compounds exhibited novel scaffolds and can be used as novel chemical probes for future studies of CB2. Importantly, our studies show that the hits obtained from the inactive CB2 model mainly act as inverse agonist(s) or neutral antagonist(s) at low concentration. Moreover, the hit from the active CB2 model also behaves as a neutral antagonist at low concentration. Our studies provide new insight leading to a better understanding of the structural and conformational differences between two states of CB2 and illuminate the effects of structure on virtual screening and drug design.
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Affiliation(s)
- Jianping Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- College of Chemistry, Leshan Normal University, Leshan, Sichuan 614004, China
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yu Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qin Tong
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mohammed Hamed Alqarni
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaojun Gou
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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22
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Stavrakov G, Philipova I, Zheleva D, Atanasova M, Konstantinov S, Doytchinova I. Docking-based Design of Galantamine Derivatives with Dual-site Binding to Acetylcholinesterase. Mol Inform 2016; 35:278-85. [PMID: 27492242 DOI: 10.1002/minf.201600041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/17/2016] [Indexed: 11/06/2022]
Abstract
The enzyme acetylcholinesterase is a key target in the treatment of Alzheimer's disease because of its ability to hydrolyze acetylcholine via the catalytic binding site and to accelerate the aggregation of amyloid-β peptide via the peripheral anionic site (PAS). Using docking-based predictions, in the present study we design 20 novel galantamine derivatives with alkylamide spacers of different length ending with aromatic fragments. The galantamine moiety blocks the catalytic site, while the terminal aromatic fragments bind in PAS. The best predicted compounds are synthesized and tested for acetylcholinesterase inhibitory activity. The experimental results confirm the predictions and show that the heptylamide spacer is of optimal length to bridge the galantamine moiety bound in the catalytic site and the aromatic fragments interacting with PAS. Among the tested terminal aromatic fragments, the phenethyl substituent is the most suitable for binding in PAS.
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Affiliation(s)
- Georgi Stavrakov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str., 1000, Sofia, Bulgaria
| | - Irena Philipova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian academy of Sciences, Acad. G. Bonchev str. 9, 1113, Sofia, Bulgaria
| | - Dimitrina Zheleva
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str., 1000, Sofia, Bulgaria
| | - Mariyana Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str., 1000, Sofia, Bulgaria
| | - Spiro Konstantinov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str., 1000, Sofia, Bulgaria
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav str., 1000, Sofia, Bulgaria.
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Discovery of novel INK4C small-molecule inhibitors to promote human and murine hematopoietic stem cell ex vivo expansion. Sci Rep 2015; 5:18115. [PMID: 26681454 PMCID: PMC4683533 DOI: 10.1038/srep18115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/12/2015] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem cells (HSCs) have emerged as promising therapeutic cell sources for high-risk hematological malignancies and immune disorders. However, their clinical use is limited by the inability to expand these cells ex vivo. Therefore, there is an urgent need to identify specific targets and effective probes that can expand HSCs. Here we report a novel class of INK4C (p18INK4C or p18) small molecule inhibitors (p18SMIs), which were initially found by in silico 3D screening. We identified a lead p18 inhibitor, XIE18-6, confirmed its p18-targeting specificity and bioactivity of promoting HSCs expansion, and then performed structure-activity relationship (SAR) studies by synthesizing a series of analogs of XIE18–6. Among these, compound 40 showed the most potent bioactivity in HSCs expansion (ED50 = 5.21 nM). We confirmed that compound 40 promoted expansion of both murine and human HSCs, and also confirmed its p18-targeting specificity. Notably, compound 40 did not show significant cytotoxicity toward 32D cells or HSCs, nor did it augment leukemia cell proliferation. Taken together, our newly discovered p18SMIs represent novel chemical agents for murine and human HSCs ex vivo expansion and also can be used as valuable chemical probes for further HSC biology research towards promising utility for therapeutic purposes.
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CB2 cannabinoid receptor agonist enantiomers HU-433 and HU-308: An inverse relationship between binding affinity and biological potency. Proc Natl Acad Sci U S A 2015; 112:8774-9. [PMID: 26124120 DOI: 10.1073/pnas.1503395112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Activation of the CB2 receptor is apparently an endogenous protective mechanism. Thus, it restrains inflammation and protects the skeleton against age-related bone loss. However, the endogenous cannabinoids, as well as Δ(9)-tetrahydrocannabinol, the main plant psychoactive constituent, activate both cannabinoid receptors, CB1 and CB2. HU-308 was among the first synthetic, selective CB2 agonists. HU-308 is antiosteoporotic and antiinflammatory. Here we show that the HU-308 enantiomer, designated HU-433, is 3-4 orders of magnitude more potent in osteoblast proliferation and osteoclast differentiation culture systems, as well as in mouse models, for the rescue of ovariectomy-induced bone loss and ear inflammation. HU-433 retains the HU-308 specificity for CB2, as shown by its failure to bind to the CB1 cannabinoid receptor, and has no activity in CB2-deficient cells and animals. Surprisingly, the CB2 binding affinity of HU-433 in terms of [(3)H]CP55,940 displacement and its effect on [(35)S]GTPγS accumulation is substantially lower compared with HU-308. A molecular-modeling analysis suggests that HU-433 and -308 have two different binding conformations within CB2, with one of them possibly responsible for the affinity difference, involving [(35)S]GTPγS and cAMP synthesis. Hence, different ligands may have different orientations relative to the same binding site. This situation questions the usefulness of universal radioligands for comparative binding studies. Moreover, orientation-targeted ligands have promising potential for the pharmacological activation of distinct processes.
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25
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Feng Z, Ma S, Hu G, Xie XQ. Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family. AAPS J 2015; 17:737-53. [PMID: 25762450 PMCID: PMC4406965 DOI: 10.1208/s12248-015-9742-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 02/16/2015] [Indexed: 11/30/2022] Open
Abstract
Metabotropic glutamate receptors (mGluR) are mainly expressed in the central nervous system (CNS) and contain eight receptor subtypes, named mGluR1 to mGluR8. The crystal structures of mGluR1 and mGluR5 that are bound with the negative allosteric modulator (NAM) were reported recently. These structures provide a basic model for all class C of G-protein coupled receptors (GPCRs) and may aid in the design of new allosteric modulators for the treatment of CNS disorders. However, these structures are only combined with NAMs in the previous reports. The conformations that are bound with positive allosteric modulator (PAM) or agonist of mGluR1/5 remain unknown. Moreover, the structural information of the other six mGluRs and the comparisons of the mGluRs family have not been explored in terms of their binding pockets, the binding modes of different compounds, and important binding residues. With these crystal structures as the starting point, we built 3D structural models for six mGluRs by using homology modeling and molecular dynamics (MD) simulations. We systematically compared their allosteric binding sites/pockets, the important residues, and the selective residues by using a series of comparable dockings with both the NAM and the PAM. Our results show that several residues played important roles for the receptors' selectivity. The observations of detailed interactions between compounds and their correspondent receptors are congruent with the specificity and potency of derivatives or compounds bioassayed in vitro. We then carried out 100 ns MD simulations of mGluR5 (residue 26-832, formed by Venus Flytrap domain, a so-called cysteine-rich domain, and 7 trans-membrane domains) bound with antagonist/NAM and with agonist/PAM. Our results show that both the NAM and the PAM seemed stable in class C GPCRs during the MD. However, the movements of "ionic lock," of trans-membrane domains, and of some activation-related residues in 7 trans-membrane domains of mGluR5 were congruent with the findings in class A GPCRs. Finally, we selected nine representative bound structures to perform 30 ns MD simulations for validating the stabilities of interactions, respectively. All these bound structures kept stable during the MD simulations, indicating that the binding poses in this present work are reasonable. We provided new insight into better understanding of the structural and functional roles of the mGluRs family and facilitated the future structure-based design of novel ligands of mGluRs family with therapeutic potential.
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Affiliation(s)
- Zhiwei Feng
- />Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
| | - Shifan Ma
- />Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
| | - Guanxing Hu
- />Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
| | - Xiang-Qun Xie
- />Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
- />Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261 USA
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Feng Z, Pearce LV, Xu X, Yang X, Yang P, Blumberg PM, Xie XQ. Structural insight into tetrameric hTRPV1 from homology modeling, molecular docking, molecular dynamics simulation, virtual screening, and bioassay validations. J Chem Inf Model 2015; 55:572-88. [PMID: 25642729 PMCID: PMC4508124 DOI: 10.1021/ci5007189] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The transient receptor potential vanilloid type 1 (TRPV1) is a heat-activated cation channel protein, which contributes to inflammation, acute and persistent pain. Antagonists of human TRPV1 (hTRPV1) represent a novel therapeutic approach for the treatment of pain. Developing various antagonists of hTRPV1, however, has been hindered by the unavailability of a 3D structure of hTRPV1. Recently, the 3D structures of rat TRPV1 (rTRPV1) in the presence and absence of ligand have been reported as determined by cryo-EM. rTRPV1 shares 85.7% sequence identity with hTRPV1. In the present work, we constructed and reported the 3D homology tetramer model of hTRPV1 based on the cryo-EM structures of rTRPV1. Molecular dynamics (MD) simulations, energy minimizations, and prescreen were applied to select and validate the best model of hTRPV1. The predicted binding pocket of hTRPV1 consists of two adjacent monomers subunits, which were congruent with the experimental rTRPV1 data and the cyro-EM structures of rTRPV1. The detailed interactions between hTRPV1 and its antagonists or agonists were characterized by molecular docking, which helped us to identify the important residues. Conformational changes of hTRPV1 upon antagonist/agonist binding were also explored by MD simulation. The different movements of compounds led to the different conformational changes of monomers in hTRPV1, indicating that TRPV1 works in a concerted way, resembling some other channel proteins such as aquaporins. We observed that the selective filter was open when hTRPV1 bound with an agonist during MD simulation. For the lower gate of hTRPV1, we observed large similarities between hTRPV1 bound with antagonist and with agonist. A five-point pharmacophore model based on several antagonists was established, and the structural model was used to screen in silico for new antagonists for hTRPV1. By using the 3D TRPV1 structural model above, the pilot in silico screening has begun to yield promising hits with activity as hTRPV1 antagonists, several of which showed substantial potency.
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Affiliation(s)
- Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Larry V. Pearce
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Xiaomeng Xu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiaole Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Peter M. Blumberg
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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27
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Gao Y, Yang P, Shen H, Yu H, Song X, Zhang L, Zhang P, Cheng H, Xie Z, Hao S, Dong F, Ma S, Ji Q, Bartlow P, Ding Y, Wang L, Liu H, Li Y, Cheng H, Miao W, Yuan W, Yuan Y, Cheng T, Xie XQ. Small-molecule inhibitors targeting INK4 protein p18(INK4C) enhance ex vivo expansion of haematopoietic stem cells. Nat Commun 2015; 6:6328. [PMID: 25692908 DOI: 10.1038/ncomms7328] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 01/16/2015] [Indexed: 02/07/2023] Open
Abstract
Among cyclin-dependent kinase inhibitors that control the G1 phase in cell cycle, only p18 and p27 can negatively regulate haematopoietic stem cell (HSC) self-renewal. In this manuscript, we demonstrate that p18 protein is a more potent inhibitor of HSC self-renewal than p27 in mouse models and its deficiency promoted HSC expansion in long-term culture. Single-cell analysis indicated that deleting p18 gene favoured self-renewing division of HSC in vitro. Based on the structure of p18 protein and in-silico screening, we further identified novel smallmolecule inhibitors that can specifically block the activity of p18 protein. Our selected lead compounds were able to expand functional HSCs in a short-term culture. Thus, these putative small-molecule inhibitors for p18 protein are valuable for further dissecting the signalling pathways of stem cell self-renewal and may help develop more effective chemical agents for therapeutic expansion of HSC.
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Affiliation(s)
- Yingdai Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Peng Yang
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Hongmei Shen
- Department of Radiation Oncology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Hui Yu
- Department of Radiation Oncology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Xianmin Song
- Department of Hematology, Changhai Hospital, Secondary Military Medical University, Shanghai 200433, China
| | - Liyan Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Peng Zhang
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Haizi Cheng
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Zhaojun Xie
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Sha Hao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qing Ji
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Patrick Bartlow
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yahui Ding
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Lirong Wang
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Haibin Liu
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yanxin Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Weimin Miao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Youzhong Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Xiang-Qun Xie
- 1] Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Drug Abuse Research, Drug Discovery Institute, Pittsburgh, Pennsylvania 15260, USA [2] Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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28
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Gianella-Borradori M, Christou I, Bataille CJR, Cross RL, Wynne GM, Greaves DR, Russell AJ. Ligand-based virtual screening identifies a family of selective cannabinoid receptor 2 agonists. Bioorg Med Chem 2015; 23:241-63. [PMID: 25487422 PMCID: PMC4346271 DOI: 10.1016/j.bmc.2014.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/31/2014] [Accepted: 11/01/2014] [Indexed: 11/17/2022]
Abstract
The cannabinoid receptor 2 (CB2R) has been linked with the regulation of inflammation, and selective receptor activation has been proposed as a target for the treatment of a range of inflammatory diseases such as atherosclerosis and arthritis. In order to identify selective CB2R agonists with appropriate physicochemical and ADME properties for future evaluation in vivo, we first performed a ligand-based virtual screen. Subsequent medicinal chemistry optimisation studies led to the identification of a new class of selective CB2R agonists. Several examples showed high levels of activity (EC50<200 nM) and binding affinity (Ki<200 nM) for the CB2R, and no detectable activity at the CB1R. The most promising example, DIAS2, also showed favourable in vitro metabolic stability and absorption properties along with a clean selectivity profile when evaluated against a panel of GPCRs and kinases.
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Affiliation(s)
- Matteo Gianella-Borradori
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ivy Christou
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Carole J R Bataille
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Rebecca L Cross
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - David R Greaves
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK.
| | - Angela J Russell
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
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29
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Feng Z, Alqarni MH, Yang P, Tong Q, Chowdhury A, Wang L, Xie XQ. Modeling, molecular dynamics simulation, and mutation validation for structure of cannabinoid receptor 2 based on known crystal structures of GPCRs. J Chem Inf Model 2014; 54:2483-99. [PMID: 25141027 PMCID: PMC4170816 DOI: 10.1021/ci5002718] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Indexed: 12/29/2022]
Abstract
The cannabinoid receptor 2 (CB2) plays an important role in the immune system. Although a few of GPCRs crystallographic structures have been reported, it is still challenging to obtain functional transmembrane proteins and high resolution X-ray crystal structures, such as for the CB2 receptor. In the present work, we used 10 reported crystal structures of GPCRs which had high sequence identities with CB2 to construct homology-based comparative CB2 models. We applied these 10 models to perform a prescreen by using a training set consisting of 20 CB2 active compounds and 980 compounds randomly selected from the National Cancer Institute (NCI) database. We then utilized the known 170 cannabinoid receptor 1 (CB1) or CB2 selective compounds for further validation. Based on the docking results, we selected one CB2 model (constructed by β1AR) that was most consistent with the known experimental data, revealing that the defined binding pocket in our CB2 model was well-correlated with the training and testing data studies. Importantly, we identified a potential allosteric binding pocket adjacent to the orthosteric ligand-binding site, which is similar to the reported allosteric pocket for sodium ion Na(+) in the A2AAR and the δ-opioid receptor. Our studies in correlation of our data with others suggested that sodium may reduce the binding affinities of endogenous agonists or its analogs to CB2. We performed a series of docking studies to compare the important residues in the binding pockets of CB2 with CB1, including antagonist, agonist, and our CB2 neutral compound (neutral antagonist) XIE35-1001. Then, we carried out 50 ns molecular dynamics (MD) simulations for the CB2 docked with SR144528 and CP55940, respectively. We found that the conformational changes of CB2 upon antagonist/agonist binding were congruent with recent reports of those for other GPCRs. Based on these results, we further examined one known residue, Val113(3.32), and predicted two new residues, Phe183 in ECL2 and Phe281(7.35), that were important for SR144528 and CP55940 binding to CB2. We then performed site-directed mutation experimental study for these residues and validated the predictions by radiometric binding affinity assay.
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Affiliation(s)
- Zhiwei Feng
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mohammed Hamed Alqarni
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Peng Yang
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Qin Tong
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Ananda Chowdhury
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Lirong Wang
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department
of Pharmaceutical Sciences and Computational Chemical
Genomics Screening Center, School of Pharmacy, Computational Drug Abuse Research
Center, Drug Discovery Institute, and Department of Computational Biology and Department
of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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30
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Alqarni M, Myint KZ, Tong Q, Yang P, Bartlow P, Wang L, Feng R, Xie XQ. Examining the critical roles of human CB2 receptor residues Valine 3.32 (113) and Leucine 5.41 (192) in ligand recognition and downstream signaling activities. Biochem Biophys Res Commun 2014; 452:334-9. [PMID: 25148941 DOI: 10.1016/j.bbrc.2014.08.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 11/19/2022]
Abstract
We performed molecular modeling and docking to predict a putative binding pocket and associated ligand-receptor interactions for human cannabinoid receptor 2 (CB2). Our data showed that two hydrophobic residues came in close contact with three structurally distinct CB2 ligands: CP-55,940, SR144528 and XIE95-26. Site-directed mutagenesis experiments and subsequent functional assays implicated the roles of Valine residue at position 3.32 (V113) and Leucine residue at position 5.41 (L192) in the ligand binding function and downstream signaling activities of the CB2 receptor. Four different point mutations were introduced to the wild type CB2 receptor: V113E, V113L, L192S and L192A. Our results showed that mutation of Val113 with a Glutamic acid and Leu192 with a Serine led to the complete loss of CB2 ligand binding as well as downstream signaling activities. Substitution of these residues with those that have similar hydrophobic side chains such as Leucine (V113L) and Alanine (L192A), however, allowed CB2 to retain both its ligand binding and signaling functions. Our modeling results validated by competition binding and site-directed mutagenesis experiments suggest that residues V113 and L192 play important roles in ligand binding and downstream signaling transduction of the CB2 receptor.
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Affiliation(s)
- Mohammed Alqarni
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Kyaw Zeyar Myint
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA; Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program, Department of Computational Biology and Structural Biology, School of Medicine, Pittsburgh, PA 15260, USA
| | - Qin Tong
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Patrick Bartlow
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Rentian Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA 15260, USA; Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program, Department of Computational Biology and Structural Biology, School of Medicine, Pittsburgh, PA 15260, USA; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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31
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Cai Z, Ouyang Q, Zeng D, Nguyen KN, Modi J, Wang L, White AG, Rogers BE, Xie XQ, Anderson CJ. 64Cu-labeled somatostatin analogues conjugated with cross-bridged phosphonate-based chelators via strain-promoted click chemistry for PET imaging: in silico through in vivo studies. J Med Chem 2014; 57:6019-29. [PMID: 24983404 PMCID: PMC4261236 DOI: 10.1021/jm500416f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Somatostatin
receptor subtype 2 (sstr2) is a G-protein-coupled
receptor (GPCR) that is overexpressed in neuroendocrine tumors. The
homology model of sstr2 was built and was used to aid the design of
new somatostatin analogues modified with phosphonate-containing cross-bridged
chelators for evaluation of using them as PET imaging radiopharmaceuticals.
The new generation chelators were conjugated to Tyr3-octreotate
(Y3-TATE) through bioorthogonal, strain-promoted alkyne azide cycloaddition
(SPAAC) to form CB-TE1A1P–DBCO–Y3-TATE (AP) and CB-TE1K1P–PEG4–DBCO–Y3-TATE
(KP) in improved yields compared to standard direct conjugation methods
of amide bond formation. Consistent with docking studies, the clicked
bioconjugates showed high binding affinities to sstr2, with Kd values ranging from 0.6 to 2.3 nM. Selected
isomers of the clicked products were used in biodistribution and PET/CT
imaging. Introduction of the bulky dibenzocyclooctyne group in AP
decreased clearance rates from circulation. However, the additional
carboxylate group and PEG linker from the KP conjugate significantly
improved labeling conditions and in vivo stability of the copper complex
and ameliorated the slower pharmacokinetics of the clicked somatostatin
analogues.
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Affiliation(s)
- Zhengxin Cai
- Department of Radiology, §Department of Pharmaceutical Sciences, Computational Chemical Genomics Screening Center, School of Pharmacy, ¶Drug Discovery Institute, ⊥Department of Pharmacology and Chemical Biology, and ▲Department of Bioengineering, University of Pittsburgh , Pittsburgh, Pennsylvania 15219, United States
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32
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Sheng S, Wang J, Wang L, Liu H, Li P, Liu M, Long C, Xie C, Xie X, Su W. Network pharmacology analyses of the antithrombotic pharmacological mechanism of Fufang Xueshuantong Capsule with experimental support using disseminated intravascular coagulation rats. JOURNAL OF ETHNOPHARMACOLOGY 2014; 154:735-744. [PMID: 24832112 DOI: 10.1016/j.jep.2014.04.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Fufang Xueshuantong (FXST) Capsule is developed on a traditional Chinese medicine remedy, with a four-herb formula of Panax notoginseng, Radix astragali, Salvia miltiorrhizae and Radix scrophulariaceae. It has been used for treatment of the clinic cardiovascular disease for many years. MATERIALS AND METHODS Due to its complexity of compositions and polypharmacological effects, it often complicates understanding of the mechanisms of action. In the present work, we have constructed an integrated model of system pharmacology to investigate the polypharmacological mechanisms of FXST formulation for treatment of thrombosis disease. RESULTS The predicted results showed that 22 ingredients in FXST were closely associated with 41 protein targets related to blood coagulation, fibrinolysis and platelet aggregation. Through analysis of the compound-protein target association, significant cross-targets between each herb indicated the multiple active chemical ingredients might interact with the same target simultaneously and thus explained the synergistic mechanisms of the principle of Traditional Chinese medicines (TCMs) as ''Jun (emperor) - Chen (minister) - Zuo (adjuvant) - Shi (courier)''. To validate the polypharmacological effects predicted by our network pharmacology (NetPharm) analysis, we have carried out experimental investigation the effects of FXST on the disorders of the blood coagulation system in a lipopolysaccharide-induced disseminated intravascular coagulation (DIC) rat model. The results showed that FXST could significantly ameliorate the activation of coagulation system, which is congruent with the cross-target prediction by NetPharm approach. CONCLUSIONS The combined investigations provide more insight into better understanding of the pharmacological mechanisms of FXST, and may also offer an alternative avenue to further explore the chemical and pharmacological basis of TCMs.
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Affiliation(s)
- Shujing Sheng
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Zhongsheng Pharmaceutical Co., Ltd., Dongguan 523325, PR China
| | - Jinxu Wang
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China; Visiting Scholar in Xie's laboratory at University of Pittsburgh, USA
| | - Lirong Wang
- Computational Chemical Genomics Screening Center, Department of Pharmaceutical Sciences, School of Pharmacy, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hong Liu
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Peibo Li
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Menghua Liu
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Chaofeng Long
- Guangdong Zhongsheng Pharmaceutical Co., Ltd., Dongguan 523325, PR China
| | - Chengshi Xie
- Guangdong Zhongsheng Pharmaceutical Co., Ltd., Dongguan 523325, PR China
| | - Xiangqun Xie
- Computational Chemical Genomics Screening Center, Department of Pharmaceutical Sciences, School of Pharmacy, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Weiwei Su
- Guangzhou Quality R & D Center of Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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33
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Malfitano AM, Basu S, Maresz K, Bifulco M, Dittel BN. What we know and do not know about the cannabinoid receptor 2 (CB2). Semin Immunol 2014; 26:369-79. [PMID: 24877594 DOI: 10.1016/j.smim.2014.04.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 12/19/2022]
Abstract
It has been well appreciated that the endocannabinoid system can regulate immune responses via the cannabinoid receptor 2 (CB2), which is primarily expressed by cells of the hematopoietic system. The endocannabinoid system is composed of receptors, ligands and enzymes controlling the synthesis and degradation of endocannabinoids. Along with endocannabinoids, both plant-derived and synthetic cannabinoids have been shown to bind to and signal through CB2 via G proteins leading to both inhibitory and stimulatory signals depending on the biological process. Because no cannabinoid ligand has been identified that only binds to CB2, the generation of mice deficient in CB2 has greatly expanded our knowledge of how CB2 contributes to immune cell development and function in health and disease. In regards to humans, genetic studies have associated CB2 with a variety of human diseases. Here, we review the endocannabinoid system with an emphasis on CB2 and its role in the immune system.
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Affiliation(s)
- Anna Maria Malfitano
- Dipartimento di Medicina e Chirurgia, Università di Salerno Facoltà di Medicina, Baronissi Campus, Baronissi 84081, (SA), Italy; Dipartimento di Farmacia, Università di Salerno, Fisciano 84084, (SA), Italy
| | - Sreemanti Basu
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
| | - Katarzyna Maresz
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA
| | - Maurizio Bifulco
- Dipartimento di Medicina e Chirurgia, Università di Salerno Facoltà di Medicina, Baronissi Campus, Baronissi 84081, (SA), Italy; Dipartimento di Farmacia, Università di Salerno, Fisciano 84084, (SA), Italy
| | - Bonnie N Dittel
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI, USA.
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34
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Chen X, Cao Y, Zhang H, Zhu Z, Liu M, Liu H, Ding X, Hong Z, Li W, Lv D, Wang L, Zhuo X, Zhang J, Xie XQ, Chai Y. Comparative normal/failing rat myocardium cell membrane chromatographic analysis system for screening specific components that counteract doxorubicin-induced heart failure from Acontium carmichaeli. Anal Chem 2014; 86:4748-57. [PMID: 24731167 PMCID: PMC4033634 DOI: 10.1021/ac500287e] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Cell membrane chromatography (CMC)
derived from pathological tissues
is ideal for screening specific components acting on specific diseases
from complex medicines owing to the maximum simulation of in vivo drug-receptor interactions. However, there are no
pathological tissue-derived CMC models that have ever been developed,
as well as no visualized affinity comparison of potential active components
between normal and pathological CMC columns. In this study, a novel
comparative normal/failing rat myocardium CMC analysis system based
on online column selection and comprehensive two-dimensional (2D)
chromatography/monolithic column/time-of-flight mass spectrometry
was developed for parallel comparison of the chromatographic behaviors
on both normal and pathological CMC columns, as well as rapid screening
of the specific therapeutic agents that counteract doxorubicin (DOX)-induced
heart failure from Acontium carmichaeli (Fuzi). In
total, 16 potential active alkaloid components with similar structures
in Fuzi were retained on both normal and failing myocardium CMC models.
Most of them had obvious decreases of affinities on failing myocardium
CMC compared with normal CMC model except for four components, talatizamine
(TALA), 14-acetyl-TALA, hetisine, and 14-benzoylneoline. One compound
TALA with the highest affinity was isolated for further in
vitro pharmacodynamic validation and target identification
to validate the screen results. Voltage-dependent K+ channel
was confirmed as a binding target of TALA and 14-acetyl-TALA with
high affinities. The online high throughput comparative CMC analysis
method is suitable for screening specific active components from herbal
medicines by increasing the specificity of screened results and can
also be applied to other biological chromatography models.
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Affiliation(s)
- Xiaofei Chen
- Department of Pharmaceutical Analysis, School of Pharmacy, Second Military Medical University , No. 325 Guohe Road, Shanghai 200433, PR China
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35
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Liu H, Wang L, Lv M, Pei R, Li P, Pei Z, Wang Y, Su W, Xie XQ. AlzPlatform: an Alzheimer's disease domain-specific chemogenomics knowledgebase for polypharmacology and target identification research. J Chem Inf Model 2014; 54:1050-60. [PMID: 24597646 PMCID: PMC4010297 DOI: 10.1021/ci500004h] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Alzheimer’s
disease (AD) is one of the most complicated progressive neurodegeneration
diseases that involve many genes, proteins, and their complex interactions.
No effective medicines or treatments are available yet to stop or
reverse the progression of the disease due to its polygenic nature.
To facilitate discovery of new AD drugs and better understand the
AD neurosignaling pathways involved, we have constructed an Alzheimer’s
disease domain-specific chemogenomics knowledgebase, AlzPlatform (www.cbligand.org/AD/) with cloud computing and sourcing
functions. AlzPlatform is implemented with powerful computational
algorithms, including our established TargetHunter, HTDocking, and
BBB Predictor for target identification and polypharmacology analysis
for AD research. The platform has assembled various AD-related chemogenomics
data records, including 928 genes and 320 proteins related to AD,
194 AD drugs approved or in clinical trials, and 405 188 chemicals
associated with 1 023 137 records of reported bioactivities
from 38 284 corresponding bioassays and 10 050 references.
Furthermore, we have demonstrated the application of the AlzPlatform
in three case studies for identification of multitargets and polypharmacology
analysis of FDA-approved drugs and also for screening and prediction
of new AD active small chemical molecules and potential novel AD drug
targets by our established TargetHunter and/or HTDocking programs.
The predictions were confirmed by reported bioactivity data and our
in vitro experimental validation. Overall, AlzPlatform will enrich
our knowledge for AD target identification, drug discovery, and polypharmacology
analyses and, also, facilitate the chemogenomics data sharing and
information exchange/communications in aid of new anti-AD drug discovery
and development.
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Affiliation(s)
- Haibin Liu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; Drug Discovery Institute; University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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36
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Design, synthesis, biological evaluation, and comparative docking study of 1,2,4-triazolones as CB1 receptor selective antagonists. Eur J Med Chem 2014; 74:73-84. [DOI: 10.1016/j.ejmech.2013.12.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 12/25/2022]
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37
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Rom S, Persidsky Y. Cannabinoid receptor 2: potential role in immunomodulation and neuroinflammation. J Neuroimmune Pharmacol 2013; 8:608-20. [PMID: 23471521 PMCID: PMC3663904 DOI: 10.1007/s11481-013-9445-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/18/2013] [Indexed: 01/02/2023]
Abstract
An accumulating body of evidence suggests that endocannabinoids and cannabinoid receptors type 1 and 2 (CB(1), CB(2)) play a significant role in physiologic and pathologic processes, including cognitive and immune functions. While the addictive properties of marijuana, an extract from the Cannabis plant, are well recognized, there is growing appreciation of the therapeutic potential of cannabinoids in multiple pathologic conditions involving chronic inflammation (inflammatory bowel disease, arthritis, autoimmune disorders, multiple sclerosis, HIV-1 infection, stroke, Alzheimer's disease to name a few), mainly mediated by CB(2) activation. Development of CB(2) agonists as therapeutic agents has been hampered by the complexity of their intracellular signaling, relative paucity of highly selective compounds and insufficient data regarding end effects in the target cells and organs. This review attempts to summarize recent advances in studies of CB(2) activation in the setting of neuroinflammation, immunomodulation and HIV-1 infection.
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Affiliation(s)
- Slava Rom
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia PA (USA)
| | - Yuri Persidsky
- Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia PA (USA)
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38
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Ouyang Q, Tong Q, Feng R, Myint KZ, Yang P, Xie XQ. Trisubstituted Sulfonamides: a New Chemotype for Development of Potent and Selective CB 2 Receptor Inverse Agonists. ACS Med Chem Lett 2013; 4:387-392. [PMID: 24729834 DOI: 10.1021/ml3004236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
An extensive exploration of the SAR of a trisubstituted sulfonamides series led to the identification of 39, which is a potent and selective CB2 receptor inverse agonist (CB2Ki = 5.4 nM, and CB1Ki = 500 nM). The functional properties measured by cAMP assays indicated that the selected compounds were CB2 inverse agonists with high potency values (34, EC50 = 8.2 nM, and 39, EC50 = 2.5 nM). Furthermore, an osteoclastogenesis bioassay indicated that trisubstituted sulfonamide compounds showed great inhibition of osteoclast formation.
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Affiliation(s)
- Qin Ouyang
- College of Pharmacy, Third Military Medical University, Chongqing 400038, China
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39
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Yang P, Wang L, Feng R, Almehizia AA, Tong Q, Myint KZ, Ouyang Q, Alqarni MH, Wang L, Xie XQ. Novel triaryl sulfonamide derivatives as selective cannabinoid receptor 2 inverse agonists and osteoclast inhibitors: discovery, optimization, and biological evaluation. J Med Chem 2013; 56:2045-58. [PMID: 23406429 DOI: 10.1021/jm3017464] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cannabinoid receptors have gained increasing attention as drug targets for developing potential therapeutic ligands. Here, we report the discovery and optimization of triaryl sulfonamides as a novel series possessing significant CB2 receptor affinity and selectivity. Four sets of triaryl ligands were designed and synthesized for further structural modifications and led to the identification of eight compounds as potent and selective CB2 inverse agonists with high binding affinity (CB2K(i) < 10 nM). Especially, compound 57 exhibited the strongest binding affinity on the CB2 receptor (CB2K(i) of 0.5 nM) and the best selectivity over the CB1 receptor (selectivity index of 2594). Importantly, 57 also showed potent inhibitory activity on osteoclast formation, and it was confirmed by a cell viability assay that the inhibition effects were not derived from the cytotoxicity. Finally, 3D QSAR studies confirmed our SAR findings that three bulky groups play an important role for CB2 receptor binding affinity.
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Affiliation(s)
- Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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40
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Ma C, Wang L, Yang P, Myint KZ, Xie XQ. LiCABEDS II. Modeling of ligand selectivity for G-protein-coupled cannabinoid receptors. J Chem Inf Model 2013; 53:11-26. [PMID: 23278450 DOI: 10.1021/ci3003914] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The cannabinoid receptor subtype 2 (CB2) is a promising therapeutic target for blood cancer, pain relief, osteoporosis, and immune system disease. The recent withdrawal of Rimonabant, which targets another closely related cannabinoid receptor (CB1), accentuates the importance of selectivity for the development of CB2 ligands in order to minimize their effects on the CB1 receptor. In our previous study, LiCABEDS (Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps) was reported as a generic ligand classification algorithm for the prediction of categorical molecular properties. Here, we report extension of the application of LiCABEDS to the modeling of cannabinoid ligand selectivity with molecular fingerprints as descriptors. The performance of LiCABEDS was systematically compared with another popular classification algorithm, support vector machine (SVM), according to prediction precision and recall rate. In addition, the examination of LiCABEDS models revealed the difference in structure diversity of CB1 and CB2 selective ligands. The structure determination from data mining could be useful for the design of novel cannabinoid lead compounds. More importantly, the potential of LiCABEDS was demonstrated through successful identification of newly synthesized CB2 selective compounds.
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Affiliation(s)
- Chao Ma
- Department of Pharmaceutical Sciences, School of Pharmacy, Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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41
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Xie XQ, Chowdhury A. Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors. Methods Enzymol 2013; 520:153-74. [PMID: 23332699 DOI: 10.1016/b978-0-12-391861-1.00007-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design.
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Affiliation(s)
- Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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42
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Yang P, Myint KZ, Tong Q, Feng R, Cao H, Almehizia AA, Alqarni MH, Wang L, Bartlow P, Gao Y, Gertsch J, Teramachi J, Kurihara N, Roodman GD, Cheng T, Xie XQ. Lead discovery, chemistry optimization, and biological evaluation studies of novel biamide derivatives as CB2 receptor inverse agonists and osteoclast inhibitors. J Med Chem 2012; 55:9973-87. [PMID: 23072339 DOI: 10.1021/jm301212u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N,N'-((4-(Dimethylamino)phenyl)methylene)bis(2-phenylacetamide) was discovered by using 3D pharmacophore database searches and was biologically confirmed as a new class of CB(2) inverse agonists. Subsequently, 52 derivatives were designed and synthesized through lead chemistry optimization by modifying the rings A-C and the core structure in further SAR studies. Five compounds were developed and also confirmed as CB(2) inverse agonists with the highest CB(2) binding affinity (CB(2)K(i) of 22-85 nM, EC(50) of 4-28 nM) and best selectivity (CB(1)/CB(2) of 235- to 909-fold). Furthermore, osteoclastogenesis bioassay indicated that PAM compounds showed great inhibition of osteoclast formation. Especially, compound 26 showed 72% inhibition activity even at the low concentration of 0.1 μM. The cytotoxicity assay suggested that the inhibition of PAM compounds on osteoclastogenesis did not result from its cytotoxicity. Therefore, these PAM derivatives could be used as potential leads for the development of a new type of antiosteoporosis agent.
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Affiliation(s)
- Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, USA
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43
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A targeted library screen reveals a new inhibitor scaffold for protein kinase D. PLoS One 2012; 7:e44653. [PMID: 23028574 PMCID: PMC3445516 DOI: 10.1371/journal.pone.0044653] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/06/2012] [Indexed: 12/31/2022] Open
Abstract
Protein kinase D (PKD) has emerged as a potential therapeutic target in multiple pathological conditions, including cancer and heart diseases. Potent and selective small molecule inhibitors of PKD are valuable for dissecting PKD-mediated cellular signaling pathways and for therapeutic application. In this study, we evaluated a targeted library of 235 small organic kinase inhibitors for PKD1 inhibitory activity at a single concentration. Twenty-eight PKD inhibitory chemotypes were identified and six exhibited excellent PKD1 selectivity. Five of the six lead structures share a common scaffold, with compound 139 being the most potent and selective for PKD vs PKC and CAMK. Compound 139 was an ATP-competitive PKD1 inhibitor with a low double-digit nanomolar potency and was also cell-active. Kinase profiling analysis identified this class of small molecules as pan-PKD inhibitors, confirmed their selectivity again PKC and CAMK, and demonstrated an overall favorable selectivity profile that could be further enhanced through structural modification. Furthermore, using a PKD homology model based on similar protein kinase structures, docking modes for compound 139 were explored and compared to literature examples of PKD inhibition. Modeling of these compounds at the ATP-binding site of PKD was used to rationalize its high potency and provide the foundation for future further optimization. Accordingly, using biochemical screening of a small number of privileged scaffolds and computational modeling, we have identified a new core structure for highly potent PKD inhibition with promising selectivity against closely related kinases. These lead structures represent an excellent starting point for the further optimization and the design of selective and therapeutically effective small molecule inhibitors of PKD.
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44
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Srinivasan A, Wang L, Cline CJ, Xie Z, Sobol RW, Xie XQ, Gold B. Identification and characterization of human apurinic/apyrimidinic endonuclease-1 inhibitors. Biochemistry 2012; 51:6246-59. [PMID: 22788932 DOI: 10.1021/bi300490r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The repair of abasic sites that arise in DNA from hydrolytic depurination/depyrimidination of the nitrogenous bases from the sugar-phosphate backbone and the action of DNA glycosylases on deaminated, oxidized, and alkylated bases are critical to cell survival. Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1; aka APE1/ref-1) is responsible for the initial removal of abasic lesions as part of the base excision repair pathway. Deletion of APE-1 activity is embryonic lethal in animals and is lethal in cells. Potential inhibitors of the repair function of APE-1 were identified based upon molecular modeling of the crystal structure of the APE-1 protein. We describe the characterization of several unique nanomolar inhibitors using two complementary biochemical screens. The most active molecules all contain a 2-methyl-4-amino-6,7-dioxolo-quinoline structure that is predicted from the modeling to anchor the compounds in the endonuclease site of the protein. The mechanism of action of the selected compounds was probed by fluorescence and competition studies, which indicate, in a specific case, direct interaction between the inhibitor and the active site of the protein. It is demonstrated that the inhibitors induce time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with their potency to inhibit APE-1 endonuclease excision. The inhibitor molecules also potentiate by 5-fold the toxicity of a DNA methylating agent that creates abasic sites. The molecules represent a new class of APE-1 inhibitors that can be used to probe the biology of this critical enzyme and to sensitize resistant tumor cells to the cytotoxicity of clinically used DNA damaging anticancer drugs.
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Affiliation(s)
- Ajay Srinivasan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Pharmacophore identification, docking and “in silico” screening for novel CDK1 inhibitors. J Mol Graph Model 2012; 37:77-86. [DOI: 10.1016/j.jmgm.2012.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 04/04/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022]
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Latest advances in novel cannabinoid CB(2) ligands for drug abuse and their therapeutic potential. Future Med Chem 2012; 4:187-204. [PMID: 22300098 DOI: 10.4155/fmc.11.179] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The field of cannabinoid (CB) drug research is experiencing a challenge as the CB(1) antagonist Rimonabant, launched in 2006 as an anorectic/anti-obesity drug, was withdrawn from the European market due to the complications of suicide and depression as side effects. There is interest in developing CB(2) drugs without CB(1) psychotropic side effects for drug-abuse treatment and therapeutic medication. The CB(1) receptor was discovered predominantly in the brain, whereas the CB(2) is mainly expressed in peripheral cells and tissues, and is involved in immune signal transduction. Conversely, the CB(2) receptor was recently detected in the CNS, for example, in the microglial cells and the neurons. While the CB(2) neurons activity remains controversial, the CB(2) receptor is an attractive therapeutic target for neuropathic pain, immune system, cancer and osteoporosis without psychoactivity. This review addresses CB drug abuse and therapeutic potential with a focus on the most recent advances on new CB(2) ligands from the literature as well as patents.
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Chowdhury A, Feng R, Tong Q, Zhang Y, Xie XQ. Mistic and TarCF as fusion protein partners for functional expression of the cannabinoid receptor 2 in Escherichia coli. Protein Expr Purif 2012; 83:128-34. [PMID: 22406258 DOI: 10.1016/j.pep.2012.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 01/14/2012] [Accepted: 01/16/2012] [Indexed: 10/28/2022]
Abstract
G protein coupled receptors (GPCRs) are key players in signal recognition and cellular communication making them important therapeutic targets. Large-scale production of these membrane proteins in their native form is crucial for understanding their mechanism of action and target-based drug design. Here we report the overexpression system for a GPCR, the cannabinoid receptor subtype 2 (CB2), in Escherichia coli C43(DE3) facilitated by two fusion partners: Mistic, an integral membrane protein expression enhancer at the N-terminal, and TarCF, a C-terminal fragment of the bacterial chemosensory transducer Tar at the C-terminal of the CB2 open reading frame region. Multiple histidine tags were added on both ends of the fusion protein to facilitate purification. Using individual and combined fusion partners, we found that CB2 fusion protein expression was maximized only when both partners were used. Variable growth and induction conditions were conducted to determine and optimize protein expression. More importantly, this fusion protein Mistic-CB2-TarCF can localize into the E. coli membrane and exhibit functional binding activities with known CB2 ligands including CP55,940, WIN55,212-2 and SR144,528. These results indicate that this novel expression and purification system provides us with a promising strategy for the preparation of biologically active GPCRs, as well as general application for the preparation of membrane-bound proteins using the two new fusion partners described.
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Affiliation(s)
- Ananda Chowdhury
- Department of Pharmaceutical Sciences, School of Pharmacy, and Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Kimura T, Yeliseev AA, Vukoti K, Rhodes SD, Cheng K, Rice KC, Gawrisch K. Recombinant cannabinoid type 2 receptor in liposome model activates g protein in response to anionic lipid constituents. J Biol Chem 2012; 287:4076-87. [PMID: 22134924 PMCID: PMC3281699 DOI: 10.1074/jbc.m111.268425] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 11/29/2011] [Indexed: 11/06/2022] Open
Abstract
Human cannabinoid type 2 (CB(2)) receptor expressed in Escherichia coli was purified and successfully reconstituted in the functional form into lipid bilayers composed of POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS), and cholesteryl hemisuccinate (CHS). Reconstitution was performed by detergent removal from the protein/lipid/detergent mixed micelles either on an adsorbent column, or by rapid dilution to below the critical micelle concentration of detergent followed by removal of detergent monomers on a concentrator. Proteoliposomes prepared at a protein/phospholipid/CHS molar ratio of 1/620-650/210-220 are free of detergent as shown by (1)H NMR, have a homogeneous protein/lipid ratio shown by isopycnic gradient ultracentrifugation, and are small in size with a mean diameter of 150-200 nm as measured by dynamic light scattering. Functional integrity of the reconstituted receptor was confirmed by quantitative binding of (2)H-labeled agonist CP-55,940-d(6) measured by (2)H magic angle spinning NMR, as well as by activation of G protein. The efficiency of G protein activation by agonist-bound CB(2) receptor was affected by negative electric surface potentials of proteoliposomes controlled by the content of anionic CHS or POPS. The activation was highest at an anionic lipid content of about 50 mol %. There was no correlation between the efficiency of G protein activation and an increase of hydrocarbon chain order induced by CHS or cholesterol. The results suggest the importance of anionic lipids in regulating signal transduction by CB(2) receptor and other class A GPCR. The successful reconstitution of milligram quantities of pure, functional CB(2) receptor enables a wide variety of structural studies.
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Affiliation(s)
- Tomohiro Kimura
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | | | - Krishna Vukoti
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | - Steven D. Rhodes
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | - Kejun Cheng
- the Chemical Biology Research Branch, NIDA and NIAAA, National Institutes of Health, Bethesda, Maryland 20852
| | - Kenner C. Rice
- the Chemical Biology Research Branch, NIDA and NIAAA, National Institutes of Health, Bethesda, Maryland 20852
| | - Klaus Gawrisch
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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Minocci D, Massei J, Martino A, Milianti M, Piz L, Di Bello D, Sbrana A, Martinotti E, Rossi AM, Nieri P. Genetic association between bipolar disorder and 524A>C (Leu133Ile) polymorphism of CNR2 gene, encoding for CB2 cannabinoid receptor. J Affect Disord 2011; 134:427-30. [PMID: 21658778 DOI: 10.1016/j.jad.2011.05.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/14/2011] [Accepted: 05/15/2011] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Several studies provided evidence that the endocannabinoid system (ECS) is involved in psychiatric diseases, like major depression, schizophrenia and bipolar disorder (BD), mainly focusing on CB1 cannabinoid receptor, and FAAH, the fatty acid amide hydrolase involved in endocannabinoid metabolism. In this study we investigated the possible association of BD with three missense SNPs, of the gene CNR2, encoding for CB2 cannabinoid receptor. METHODS The possible association between BD and three CNR2 missense SNPs, namely rs2501432 (315A>G; Arg63Gln), rs41311993 (524C>A; Leu133Ile) and rs2229579 (1073C>T; Tyr316His), was investigated through a case-control study. Eighty patients and one hundred and sixty healthy subjects were recruited. Allele Specific Oligonucleotide (ASO)-PCR and restriction fragment length polymorphism (RFLP) methods were used for genotyping. RESULTS A statistically significant association was found between BD and the CNR2 524C>A; Leu133Ile (P(χ(2)) = 0.001; OR = 4.74; 95% C.I. = 2.52-10.50) while no statistically significant difference between BD and control group was observed for the other two SNPs. CONCLUSION Though further investigations are necessary to confirm this data, our results suggest that CB2 cannabinoid receptor may play a role in BD.
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MESH Headings
- Adult
- Alleles
- Amidohydrolases/genetics
- Amidohydrolases/metabolism
- Bipolar Disorder/genetics
- Cannabinoid Receptor Modulators/genetics
- Case-Control Studies
- Depressive Disorder, Major/genetics
- Female
- Genetic Predisposition to Disease
- Genotype
- Humans
- Male
- Mutation, Missense
- Polymorphism, Genetic
- Polymorphism, Restriction Fragment Length
- Polymorphism, Single Nucleotide
- Receptor, Cannabinoid, CB1/genetics
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB2/genetics
- Receptor, Cannabinoid, CB2/metabolism
- Schizophrenia/genetics
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Affiliation(s)
- D Minocci
- Dept of Psychiatry, Unit of Neurobiology, Pharmacology and Biotechnology, University of Pisa, Pisa, Italy
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