1
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Ullah A, Ullah S, Halim SA, Waqas M, Ali B, Ataya FS, El-Sabbagh NM, Batiha GES, Avula SK, Csuk R, Khan A, Al-Harrasi A. Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques. Sci Rep 2024; 14:3590. [PMID: 38351259 PMCID: PMC10864406 DOI: 10.1038/s41598-024-53911-6] [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: 08/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 appeared as a highly contagious disease after its outbreak in December 2019 by the virus, named SARS-CoV-2. The threat, which originated in Wuhan, China, swiftly became an international emergency. Among different genomic products, spike protein of virus plays a crucial role in the initiation of the infection by binding to the human lung cells, therefore, SARS-CoV-2's spike protein is a promising therapeutic target. Using a combination of a structure-based virtual screening and biochemical assay, this study seeks possible therapeutic candidates that specifically target the viral spike protein. A database of ~ 850 naturally derived compounds was screened against SARS-CoV-2 spike protein to find natural inhibitors. Using virtual screening and inhibitory experiments, we identified acetyl 11-keto-boswellic acid (AKBA) as a promising molecule for spike protein, which encouraged us to scan the rest of AKBA derivatives in our in-house database via 2D-similarity searching. Later 19 compounds with > 85% similarity with AKBA were selected and docked with receptor binding domain (RBD) of spike protein. Those hits declared significant interactions at the RBD interface, best possess and excellent drug-likeness and pharmacokinetics properties with high gastrointestinal absorption (GIA) without toxicity and allergenicity. Our in-silico observations were eventually validated by in vitro bioassay, interestingly, 10 compounds (A3, A4, C3, C6A, C6B, C6C, C6E, C6H, C6I, and C6J) displayed significant inhibitory ability with good percent inhibition (range: > 72-90). The compounds C3 (90.00%), C6E (91.00%), C6C (87.20%), and C6D (86.23%) demonstrated excellent anti-SARS CoV-2 spike protein activities. The docking interaction of high percent inhibition of inhibitor compounds C3 and C6E was confirmed by MD Simulation. In the molecular dynamics simulation, we observed the stable dynamics of spike protein inhibitor complexes and the influence of inhibitor binding on the protein's conformational arrangements. The binding free energy ΔGTOTAL of C3 (-38.0 ± 0.08 kcal/mol) and C6E (-41.98 ± 0.08 kcal/mol) respectively indicate a strong binding affinity to Spike protein active pocket. These findings demonstrate that these molecules particularly inhibit the function of spike protein and, therefore have the potential to be evaluated as drug candidates against SARS-CoV-2.
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Affiliation(s)
- Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Pakistan
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Nasser M El-Sabbagh
- Department of Veterinary Pharmacology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Satya Kumar Avula
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Rene Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120, Halle (Saale), Germany
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
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2
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Mathur S, Gawas C, Ahmad IZ, Wani M, Tabassum H. Neurodegenerative disorders: Assessing the impact of natural vs drug-induced treatment options. Aging Med (Milton) 2023; 6:82-97. [PMID: 36911087 PMCID: PMC10000287 DOI: 10.1002/agm2.12243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/29/2023] [Indexed: 02/24/2023] Open
Abstract
Neurodegenerative illnesses refer to the gradual, cumulative loss of neural activity. Neurological conditions are considered to be the second leading cause of mortality in the modern world and the two most prevalent ones are Parkinson's disease and Alzheimer's disease. The negative side effects of pharmaceutical use are a major global concern, despite the availability of many different treatments for therapy. We concentrated on different types of neurological problems and their influence on targets, in vitro, in vivo, and in silico methods toward neurological disorders, as well as the molecular approaches influencing the same, in the first half of the review. The bulk of the second half of the review focuses on the many categories of treatment possibilities, including natural and artificial. Nevertheless, herbal treatment solutions are piquing scholarly attention due to their anti-oxidative properties and accessibility. However, more quality investigations and innovations are undoubtedly needed to back up these conclusions.
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Affiliation(s)
- Sakshi Mathur
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | - Chaitali Gawas
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | | | - Minal Wani
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | - Heena Tabassum
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
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3
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Ferrari E, Scheggia D, Zianni E, Italia M, Brumana M, Palazzolo L, Parravicini C, Pilotto A, Padovani A, Marcello E, Eberini I, Calabresi P, Diluca M, Gardoni F. Rabphilin-3A as a Novel Target to Reverse α-synuclein-induced Synaptic Loss in Parkinson's Disease. Pharmacol Res 2022; 183:106375. [PMID: 35918045 DOI: 10.1016/j.phrs.2022.106375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 10/16/2022]
Abstract
Toxic aggregates of α-synuclein (αsyn) are considered key drivers of Parkinson's disease (PD) pathology. In early PD, αsyn induces synaptic dysfunction also modulating the glutamatergic neurotransmission. However, a more detailed understanding of the molecular mechanisms underlying αsyn-triggered synaptic failure is required to design novel therapeutic interventions. Here, we described the role of Rabphilin-3A (Rph3A) as novel target to counteract αsyn-induced synaptic loss in PD. Rph3A is a synaptic protein interacting with αsyn and involved in stabilizing dendritic spines and in promoting the synaptic retention of NMDA-type glutamate receptors. We found that in vivo intrastriatal injection of αsyn-preformed fibrils in mice induces the early loss of striatal synapses associated with decreased synaptic levels of Rph3A and impaired Rph3A/NMDA receptors interaction. Modulating Rph3A striatal expression or interfering with the Rph3A/αsyn complex with a small molecule prevented dendritic spine loss and rescued associated early motor defects in αsyn-injected mice. Notably, the same experimental approaches prevented αsyn-induced synaptic loss in vitro in primary hippocampal neurons. Overall, these findings indicate that approaches aimed at restoring Rph3A synaptic functions can slow down the early synaptic detrimental effects of αsyn aggregates in PD.
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Affiliation(s)
- Elena Ferrari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Diego Scheggia
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Elisa Zianni
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Maria Italia
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Marta Brumana
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Luca Palazzolo
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Chiara Parravicini
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Andrea Pilotto
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, 25123, Brescia, Italy.
| | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, 25123, Brescia, Italy.
| | - Elena Marcello
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Paolo Calabresi
- Sezione di Neurologia, Dipartimento di Neuroscienze, Facoltà di Medicina e Chirurgia, Università Cattolica del Sacro Cuore, Rome, Italy; Clinica Neurologica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
| | - Monica Diluca
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
| | - Fabrizio Gardoni
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy.
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4
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Alqahtani A. Application of Artificial Intelligence in Discovery and Development of Anticancer and Antidiabetic Therapeutic Agents. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:6201067. [PMID: 35509623 PMCID: PMC9060979 DOI: 10.1155/2022/6201067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022]
Abstract
Spectacular developments in molecular and cellular biology have led to important discoveries in cancer research. Despite cancer is one of the major causes of morbidity and mortality globally, diabetes is one of the most leading sources of group of disorders. Artificial intelligence (AI) has been considered the fourth industrial revolution machine. The most major hurdles in drug discovery and development are the time and expenditures required to sustain the drug research pipeline. Large amounts of data can be explored and generated by AI, which can then be converted into useful knowledge. Because of this, the world's largest drug companies have already begun to use AI in their drug development research. In the present era, AI has a huge amount of potential for the rapid discovery and development of new anticancer drugs. Clinical studies, electronic medical records, high-resolution medical imaging, and genomic assessments are just a few of the tools that could aid drug development. Large data sets are available to researchers in the pharmaceutical and medical fields, which can be analyzed by advanced AI systems. This review looked at how computational biology and AI technologies may be utilized in cancer precision drug development by combining knowledge of cancer medicines, drug resistance, and structural biology. This review also highlighted a realistic assessment of the potential for AI in understanding and managing diabetes.
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Affiliation(s)
- Amal Alqahtani
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541, Saudi Arabia
- Department of Basic Sciences, Deanship of Preparatory Year and Supporting Studies, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 34212, Saudi Arabia
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5
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Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK. Structure-Based Design of a Chemical Probe Set for the 5-HT 5A Serotonin Receptor. J Med Chem 2022; 65:4201-4217. [PMID: 35195401 DOI: 10.1021/acs.jmedchem.1c02031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5-HT5A receptor (5-HT5AR), for which no selective agonists and a few antagonists exist, remains the least understood serotonin receptor. A single commercial antagonist, SB-699551, has been widely used to investigate the 5-HT5AR function in neurological disorders, including pain, but this molecule has substantial liabilities as a chemical probe. Accordingly, we sought to develop an internally controlled probe set. Docking over 6 million molecules against a 5-HT5AR homology model identified 5 mid-μM ligands, one of which was optimized to UCSF678, a 42 nM arrestin-biased partial agonist at the 5-HT5AR with a more restricted off-target profile and decreased assay liabilities versus SB-699551. Site-directed mutagenesis supported the docked pose of UCSF678. Surprisingly, analogs of UCSF678 that lost the 5-HT5AR activity revealed that 5-HT5AR engagement is nonessential for alleviating pain, contrary to studies with less-selective ligands. UCSF678 and analogs constitute a selective probe set with which to study the function of the 5-HT5AR.
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Affiliation(s)
- Anat Levit Kaplan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Ryan T Strachan
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Joao M Braz
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Veronica Craik
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Samuel Slocum
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Thomas Mangano
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Vanessa Amabo
- National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
| | - Allan I Basbaum
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bryan L Roth
- Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States
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6
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Wen ZQ, Liu D, Zhang Y, Cai ZJ, Xiao WF, Li YS. G Protein-Coupled Receptors in Osteoarthritis: A Novel Perspective on Pathogenesis and Treatment. Front Cell Dev Biol 2021; 9:758220. [PMID: 34746150 PMCID: PMC8564363 DOI: 10.3389/fcell.2021.758220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/27/2021] [Indexed: 11/30/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are transmembrane receptor proteins that trigger numerous intracellular signaling pathways in response to the extracellular stimuli. The GPCRs superfamily contains enormous structural and functional diversity and mediates extensive biological processes. Until now, critical roles have been established in many diseases, including osteoarthritis (OA). Existing studies have shown that GPCRs play an important role in some OA-related pathogenesis, such as cartilage matrix degradation, synovitis, subchondral bone remodeling, and osteophyte formation. However, current pharmacological treatments are mostly symptomatic and there is a paucity of disease-modifying OA drugs so far. Targeting GPCRs is capable of inhibiting cartilage matrix degradation and synovitis and up-regulating cartilage matrix synthesis, providing a new therapeutic strategy for OA. In this review, we have comprehensively summarized the structures, biofunctions, and the novel roles of GPCRs in the pathogenesis and treatment of OA, which is expected to lay the foundation for the development of novel therapeutics against OA. Even though targeting GPCRs may ameliorate OA progression, many GPCRs-related therapeutic strategies are still in the pre-clinical stage and require further investigation.
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Affiliation(s)
- Ze-Qin Wen
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China
| | - Di Liu
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zhang
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zi-Jun Cai
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China
| | - Wen-Feng Xiao
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yu-Sheng Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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7
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Abstract
Structure-based docking screens of large compound libraries have become common in early drug and probe discovery. As computer efficiency has improved and compound libraries have grown, the ability to screen hundreds of millions, and even billions, of compounds has become feasible for modest-sized computer clusters. This allows the rapid and cost-effective exploration and categorization of vast chemical space into a subset enriched with potential hits for a given target. To accomplish this goal at speed, approximations are used that result in undersampling of possible configurations and inaccurate predictions of absolute binding energies. Accordingly, it is important to establish controls, as are common in other fields, to enhance the likelihood of success in spite of these challenges. Here we outline best practices and control docking calculations that help evaluate docking parameters for a given target prior to undertaking a large-scale prospective screen, with exemplification in one particular target, the melatonin receptor, where following this procedure led to direct docking hits with activities in the subnanomolar range. Additional controls are suggested to ensure specific activity for experimentally validated hit compounds. These guidelines should be useful regardless of the docking software used. Docking software described in the outlined protocol (DOCK3.7) is made freely available for academic research to explore new hits for a range of targets.
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8
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Doan P, Nguyen P, Murugesan A, Subramanian K, Konda Mani S, Kalimuthu V, Abraham BG, Stringer BW, Balamuthu K, Yli-Harja O, Kandhavelu M. Targeting Orphan G Protein-Coupled Receptor 17 with T0 Ligand Impairs Glioblastoma Growth. Cancers (Basel) 2021; 13:cancers13153773. [PMID: 34359676 PMCID: PMC8345100 DOI: 10.3390/cancers13153773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Glioblastoma multiforme (GBM), or glioblastoma chemotherapy, has one of the poorest improvements across all types of cancers. Despite the different rationales explored in targeted therapy for taming the GBM aggressiveness, its phenotypic plasticity, drug toxicity, and adaptive resistance mechanisms pose many challenges in finding an effective cure. Our manuscript reports the expression and prognostic role of orphan receptor GPR17 in glioma, the molecular mechanism of action of the novel ligand of GPR17, and provides evidence how the T0 agonist promotes glioblastoma cell death through modulation of the MAPK/ERK, PI3K–Akt, STAT, and NF-κB pathways. The highlights are as follows: GPR17 expression is associated with greater survival for both low-grade glioma (LGG) and GBM; GA-T0, a potent GPR17 receptor agonist, causes significant GBM cell death and apoptosis; GPR17 signaling promotes cell cycle arrest at the G1 phase in GBM cells; key genes are modulated in the signaling pathways that inhibit GBM cell proliferation; and GA-T0 crosses the blood–brain barrier and reduces tumor volume. Abstract Glioblastoma, an invasive high-grade brain cancer, exhibits numerous treatment challenges. Amongst the current therapies, targeting functional receptors and active signaling pathways were found to be a potential approach for treating GBM. We exploited the role of endogenous expression of GPR17, a G protein-coupled receptor (GPCR), with agonist GA-T0 in the survival and treatment of GBM. RNA sequencing was performed to understand the association of GPR17 expression with LGG and GBM. RT-PCR and immunoblotting were performed to confirm the endogenous expression of GPR17 mRNA and its encoded protein. Biological functions of GPR17 in the GBM cells was assessed by in vitro analysis. HPLC and histopathology in wild mice and an acute-toxicity analysis in a patient-derived xenograft model were performed to understand the clinical implication of GA-T0 targeting GPR17. We observed the upregulation of GPR17 in association with improved survival of LGG and GBM, confirming it as a predictive biomarker. GA-T0-stimulated GPR17 leads to the inhibition of cyclic AMP and calcium flux. GPR17 signaling activation enhances cytotoxicity against GBM cells and, in patient tissue-derived mesenchymal subtype GBM cells, induces apoptosis and prevents proliferation by stoppage of the cell cycle at the G1 phase. Modulation of the key genes involved in DNA damage, cell cycle arrest, and in several signaling pathways, including MAPK/ERK, PI3K–Akt, STAT, and NF-κB, prevents tumor regression. In vivo activation of GPR17 by GA-T0 reduces the tumor volume, uncovering the potential of GA-T0–GPR17 as a targeted therapy for GBM treatment. Conclusion: Our analysis suggests that GA-T0 targeting the GPR17 receptor presents a novel therapy for treating glioblastoma.
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Affiliation(s)
- Phuong Doan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | - Phung Nguyen
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
- Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Kumar Subramanian
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
| | | | - Vignesh Kalimuthu
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India; (V.K.); (K.B.)
| | - Bobin George Abraham
- Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland;
| | - Brett W. Stringer
- College of Medicine and Public Health, Flinders University, Sturt Rd., Bedford Park, SA 5042, Australia;
| | - Kadalmani Balamuthu
- Department of Animal Science, Bharathidasan University, Tiruchirappalli 620024, India; (V.K.); (K.B.)
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland;
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; (P.D.); (P.N.); (A.M.); (K.S.)
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön Katu 34, 33520 Tampere, Finland
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
- Correspondence: ; Tel.: +358-504721724
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9
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Nguyen P, Doan P, Rimpilainen T, Konda Mani S, Murugesan A, Yli-Harja O, Candeias NR, Kandhavelu M. Synthesis and Preclinical Validation of Novel Indole Derivatives as a GPR17 Agonist for Glioblastoma Treatment. J Med Chem 2021; 64:10908-10918. [PMID: 34304559 PMCID: PMC8389915 DOI: 10.1021/acs.jmedchem.1c00277] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The discovery of a potential ligand-targeting G protein-coupled receptor 17 (GPR17) is important for developing chemotherapeutic agents against glioblastoma multiforme (GBM). We used the integration of ligand- and structure-based cheminformatics and experimental approaches for identifying the potential GPR17 ligand for GBM treatment. Here, we identified a novel indoline-derived phenolic Mannich base as an activator of GPR17 using molecular docking of over 6000 indoline derivatives. One of the top 10 hit molecules, CHBC, with a glide score of -8.390 was synthesized through a multicomponent Petasis borono-Mannich reaction. The CHBC-GPR17 interaction leads to a rapid decrease of cAMP and Ca2+. CHBC exhibits the cytotoxicity effect on GBM cells in a dose-dependent manner with an IC50 of 85 μM, whereas the known agonist MDL29,951 showed a negligible effect. Our findings suggest that the phenolic Mannich base could be a better GPR17 agonist than MDL29,951, and further uncovering their pharmacological properties could potentiate an inventive GBM treatment.
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Affiliation(s)
- Phung Nguyen
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland.,BioMeditech and Tays Cancer Center, Tampere University, Hospital, P.O. Box 553, 33101 Tampere, Finland
| | - Phuong Doan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland.,BioMeditech and Tays Cancer Center, Tampere University, Hospital, P.O. Box 553, 33101 Tampere, Finland
| | - Tatu Rimpilainen
- Faculty of Engineering and Natural Sciences, Tampere University, 33101 Tampere, Finland
| | - Saravanan Konda Mani
- Scigen Research and Innovation Pvt Ltd, Periyar Technology Business Incubator, Thanjavur, Tamil Nadu 613403, India
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland.,Department of Biotechnology, Lady Doak College, Thallakulam, 625002 Madurai, India
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland.,Institute for Systems Biology, 1441N 34th Street, Seattle, Washington 98103-8904, United States
| | - Nuno R Candeias
- Faculty of Engineering and Natural Sciences, Tampere University, 33101 Tampere, Finland.,LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, 33720 Tampere, Finland.,BioMeditech and Tays Cancer Center, Tampere University, Hospital, P.O. Box 553, 33101 Tampere, Finland
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10
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Mutharasu G, Murugesan A, Konda Mani S, Yli-Harja O, Kandhavelu M. Transcriptomic analysis of glioblastoma multiforme providing new insights into GPR17 signaling communication. J Biomol Struct Dyn 2020; 40:2586-2599. [PMID: 33140689 DOI: 10.1080/07391102.2020.1841029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glioblastoma Multiforme (GBM) is one of the most aggressive malignant tumors in the central nervous system, which arises due to the failure or crosstalk in the signaling networks. GPR17, an orphan G protein-coupled receptor is anticipated to be associated with the biology of the GBM disease progression. In the present study, we have identified the differential expressions of around 170 genes along with GPR17 through the RNA-Seq analysis of 169 GBM samples. Coordinated expression patterns of all other gene products with this receptor were analysed using gene ontology and protein-protein interaction data. Several crucial signaling components and genes that play a significant role in tumor progression have been identified among which GPR17 was found to be significantly interacting with about 30 different pathways. High-throughput molecular docking of GPR17 by homology-based model against differentially expressed proteins, showed effective recognition and binding of PX, SH3, and Ig-like domains besides Gi protein. Pathways of PI3, Src, Ptdn, Ras, cytoplasmic tyrosine kinases, phospholipases, nexins and other proteins possessing these structural domains are identified as critical signaling components of the complex GBM signaling network. Our findings also provide a mechanistic insight of GPR17-T0510-3657 interaction, which potentially regulates the interaction of PX domain and helical mPTS recognition domain-containing proteins. Overall, our results demonstrate that GPR17 mediated signaling networks could be used as a therapeutic target for GBM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gnanavel Mutharasu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Akshaya Murugesan
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Molecular Signalling Lab, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, India
| | - Saravanan Konda Mani
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Olli Yli-Harja
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Computaional Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Institute for Systems Biology, Seattle, WA, USA
| | - Meenakshisundaram Kandhavelu
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Molecular Signalling Lab, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Science Center, Tampere University Hospital, Tampere, Finland
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11
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Development of the first in vivo GPR17 ligand through an iterative drug discovery pipeline: A novel disease-modifying strategy for multiple sclerosis. PLoS One 2020; 15:e0231483. [PMID: 32320409 PMCID: PMC7176092 DOI: 10.1371/journal.pone.0231483] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
The GPR17 receptor, expressed on oligodendroglial precursors (OPCs, the myelin producing cells), has emerged as an attractive target for a pro-myelinating strategy in multiple sclerosis (MS). However, the proof-of-concept that selective GPR17 ligands actually exert protective activity in vivo is still missing. Here, we exploited an iterative drug discovery pipeline to prioritize novel and selective GPR17 pro-myelinating agents out of more than 1,000,000 compounds. We first performed an in silico high-throughput screening on GPR17 structural model to identify three chemically-diverse ligand families that were then combinatorially exploded and refined. Top-scoring compounds were sequentially tested on reference pharmacological in vitro assays with increasing complexity, ending with myelinating OPC-neuron co-cultures. Successful ligands were filtered through in silico simulations of metabolism and pharmacokinetics, to select the most promising hits, whose dose and ability to target the central nervous system were then determined in vivo. Finally, we show that, when administered according to a preventive protocol, one of them (named by us as galinex) is able to significantly delay the onset of experimental autoimmune encephalomyelitis (EAE), a mouse model of MS. This outcome validates the predictivity of our pipeline to identify novel MS-modifying agents.
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12
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Lecca D, Raffaele S, Abbracchio MP, Fumagalli M. Regulation and signaling of the GPR17 receptor in oligodendroglial cells. Glia 2020; 68:1957-1967. [PMID: 32086854 DOI: 10.1002/glia.23807] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/14/2022]
Abstract
Remyelination, namely, the formation of new myelin sheaths around denuded axons, counteracts axonal degeneration and restores neuronal function. Considerable advances have been made in understanding this regenerative process that often fails in diseases like multiple sclerosis, leaving axons demyelinated and vulnerable to damage, thus contributing to disease progression. The identification of the membrane receptor GPR17 on a subset of oligodendrocyte precursor cells (OPCs), which mediate remyelination in the adult central nervous system (CNS), has led to a huge amount of evidence that validated this receptor as a new attractive target for remyelinating therapies. Here, we summarize the role of GPR17 in OPC function, myelination and remyelination, describing its atypical pharmacology, its downstream signaling, and the genetic and epigenetic factors modulating its activity. We also highlight crucial insights into GPR17 pathophysiology coming from the demonstration that oligodendrocyte injury, associated with inflammation in chronic neurodegenerative conditions, is invariably characterized by abnormal and persistent GPR17 upregulation, which, in turn, is accompanied by a block of OPCs at immature premyelinating stages. Finally, we discuss the current literature in light of the potential exploitment of GPR17 as a therapeutic target to promote remyelination.
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Affiliation(s)
- Davide Lecca
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefano Raffaele
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Maria P Abbracchio
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Marta Fumagalli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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13
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Capelli D, Parravicini C, Pochetti G, Montanari R, Temporini C, Rabuffetti M, Trincavelli ML, Daniele S, Fumagalli M, Saporiti S, Bonfanti E, Abbracchio MP, Eberini I, Ceruti S, Calleri E, Capaldi S. Surface Plasmon Resonance as a Tool for Ligand Binding Investigation of Engineered GPR17 Receptor, a G Protein Coupled Receptor Involved in Myelination. Front Chem 2020; 7:910. [PMID: 31998697 PMCID: PMC6966494 DOI: 10.3389/fchem.2019.00910] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/16/2019] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to investigate the potential of surface plasmon resonance (SPR) spectroscopy for the measurement of real-time ligand-binding affinities and kinetic parameters for GPR17, a G protein-coupled receptor (GPCR) of major interest in medicinal chemistry as potential target in demyelinating diseases. The receptor was directly captured, in a single-step, from solubilized membrane extracts on the sensor chip through a covalently bound anti-6x-His-antibody and retained its ligand binding activity for over 24 h. Furthermore, our experimental setup made possible, after a mild regeneration step, to remove the bound receptor without damaging the antibody, and thus to reuse many times the same chip. Two engineered variants of GPR17, designed for crystallographic studies, were expressed in insect cells, extracted from crude membranes and analyzed for their binding with two high affinity ligands: the antagonist Cangrelor and the agonist Asinex 1. The calculated kinetic parameters and binding constants of ligands were in good agreement with those reported from activity assays and highlighted a possible functional role of the N-terminal residues of the receptor in ligand recognition and binding. Validation of SPR results was obtained by docking and molecular dynamics of GPR17-ligands interactions and by functional in vitro studies. The latter allowed us to confirm that Asinex 1 behaves as GPR17 receptor agonist, inhibits forskolin-stimulated adenylyl cyclase pathway and promotes oligodendrocyte precursor cell maturation and myelinating ability.
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Affiliation(s)
- Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Chiara Parravicini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Marco Rabuffetti
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | | | | | - Marta Fumagalli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Simona Saporiti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Bonfanti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Maria P Abbracchio
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences, Data Science Research Center, Università degli Studi di Milano, Milan, Italy
| | - Stefania Ceruti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Enrica Calleri
- Department of Drug Sciences, University of Pavia, Pavia, Italy
| | - Stefano Capaldi
- Department of Biotechnology, University of Verona, Verona, Italy
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14
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Theoretical and Experimental Approaches Aimed at Drug Design Targeting Neurodegenerative Diseases. Processes (Basel) 2019. [DOI: 10.3390/pr7120940] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In recent years, green chemistry has been strengthening, showing how basic and applied sciences advance globally, protecting the environment and human health. A clear example of this evolution is the synergy that now exists between theoretical and computational methods to design new drugs in the most efficient possible way, using the minimum of reagents and obtaining the maximum yield. The development of compounds with potential therapeutic activity against multiple targets associated with neurodegenerative diseases/disorders (NDD) such as Alzheimer’s disease is a hot topic in medical chemistry, where different scientists from various disciplines collaborate to find safe, active, and effective drugs. NDD are a public health problem, affecting mainly the population over 60 years old. To generate significant progress in the pharmacological treatment of NDD, it is necessary to employ different experimental strategies of green chemistry, medical chemistry, and molecular biology, coupled with computational and theoretical approaches such as molecular simulations and chemoinformatics, all framed in the rational drug design targeting NDD. Here, we review how green chemistry and computational approaches have been used to develop new compounds with the potential application against NDD, as well as the challenges and new directions of the drug development multidisciplinary process.
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15
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Wang T, Liu XH, Guan J, Ge S, Wu MB, Lin JP, Yang LR. Advancement of multi-target drug discoveries and promising applications in the field of Alzheimer's disease. Eur J Med Chem 2019; 169:200-223. [PMID: 30884327 DOI: 10.1016/j.ejmech.2019.02.076] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/12/2019] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Complex diseases (e.g., Alzheimer's disease) or infectious diseases are usually caused by complicated and varied factors, including environmental and genetic factors. Multi-target (polypharmacology) drugs have been suggested and have emerged as powerful and promising alternative paradigms in modern medicinal chemistry for the development of versatile chemotherapeutic agents to solve these medical challenges. The multifunctional agents capable of modulating multiple biological targets simultaneously display great advantages of higher efficacy, improved safety profile, and simpler administration compared to single-targeted agents. Therefore, multifunctional agents would certainly open novel avenues to rationally design the next generation of more effective but less toxic therapeutic agents. Herein, the authors review the recent progress made in the discovery and design processes of selective multi-targeted agents, especially the successful application of multi-target drugs for the treatment of Alzheimer's disease.
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Affiliation(s)
- Tao Wang
- School of Biological Science, Jining Medical University, Jining, China; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Jing Guan
- School of Biological Science, Jining Medical University, Jining, China
| | - Shun Ge
- School of Biological Science, Jining Medical University, Jining, China.
| | - Mian-Bin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China; Zhejiang Key Laboratory of Antifungal Drugs, Taizhou, 318000, China
| | - Jian-Ping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Li-Rong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
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Marucci G, Dal Ben D, Lambertucci C, Martí Navia A, Spinaci A, Volpini R, Buccioni M. GPR17 receptor modulators and their therapeutic implications: review of recent patents. Expert Opin Ther Pat 2019; 29:85-95. [PMID: 30640576 DOI: 10.1080/13543776.2019.1568990] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION The GPR17 receptor, phylogenetically related to both purinergic P2Y and CysLT receptors, is mainly expressed in the CNS and, in general, in organs that can typically undergo ischemic damage. This receptor is involved in various pathologies including stroke, brain and spinal cord trauma, multiple sclerosis and in all diseases characterized by neuronal and myelin dysfunction. Therefore, there is a strong needed to identify molecules capable of binding specifically to GPR17 receptors. AREAS COVERED The review provides a summary of patents, published between 2009 and 2018, on chemicals and biologics and their clinical use. In this work, information is reported about the representative structures and biological activity of recently developed GPR17 receptor ligands. EXPERT OPINION The GPR17 receptor is an enigmatic receptor and an interesting therapeutic target in a variety of brain disorders and demyelinating diseases such as multiple sclerosis, stroke, schizophrenia, and depression. The modulation of this receptor could also be potentially useful in obesity treatment. Unfortunately, so far, there are no compounds under investigation in clinical trials but many researchers and companies are investing in the discovery of future potential GPR17 receptor drugs.
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Affiliation(s)
- Gabriella Marucci
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Diego Dal Ben
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Catia Lambertucci
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Aleix Martí Navia
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Andrea Spinaci
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Rosaria Volpini
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
| | - Michela Buccioni
- a School of Pharmacy, Medicinal Chemistry Unit , University of Camerino , Camerino , Italy
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17
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Makhouri FR, Ghasemi JB. In Silico Studies in Drug Research Against Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:664-725. [PMID: 28831921 PMCID: PMC6080098 DOI: 10.2174/1570159x15666170823095628] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/16/2017] [Indexed: 01/14/2023] Open
Abstract
Background Neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis, Parkinson's disease (PD), spinal cerebellar ataxias, and spinal and bulbar muscular atrophy are described by slow and selective degeneration of neurons and axons in the central nervous system (CNS) and constitute one of the major challenges of modern medicine. Computer-aided or in silico drug design methods have matured into powerful tools for reducing the number of ligands that should be screened in experimental assays. Methods In the present review, the authors provide a basic background about neurodegenerative diseases and in silico techniques in the drug research. Furthermore, they review the various in silico studies reported against various targets in neurodegenerative diseases, including homology modeling, molecular docking, virtual high-throughput screening, quantitative structure activity relationship (QSAR), hologram quantitative structure activity relationship (HQSAR), 3D pharmacophore mapping, proteochemometrics modeling (PCM), fingerprints, fragment-based drug discovery, Monte Carlo simulation, molecular dynamic (MD) simulation, quantum-mechanical methods for drug design, support vector machines, and machine learning approaches. Results Detailed analysis of the recently reported case studies revealed that the majority of them use a sequential combination of ligand and structure-based virtual screening techniques, with particular focus on pharmacophore models and the docking approach. Conclusion Neurodegenerative diseases have a multifactorial pathoetiological origin, so scientists have become persuaded that a multi-target therapeutic strategy aimed at the simultaneous targeting of multiple proteins (and therefore etiologies) involved in the development of a disease is recommended in future.
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Affiliation(s)
| | - Jahan B Ghasemi
- Chemistry Department, Faculty of Sciences, University of Tehran, Tehran, Iran
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18
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Baig MH, Ahmad K, Rabbani G, Danishuddin M, Choi I. Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders. Curr Neuropharmacol 2018; 16:740-748. [PMID: 29046156 PMCID: PMC6080097 DOI: 10.2174/1570159x15666171016163510] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/24/2017] [Accepted: 10/10/2017] [Indexed: 12/11/2022] Open
Abstract
Background Neurodegenerative disorders (NDs) are diverse group of disorders characterized by escalating loss of neurons (structural and functional). The development of potential therapeutics for NDs presents an important challenge, as traditional treatments are inefficient and usually are unable to stop or retard the process of neurodegeneration. Computer-Aided Drug Design (CADD) has emerged as an efficient means of developing candidate drugs for the treatment of many disease types. Applications of CADD approach to drug discovery are progressing day by day. The recent tendency in drug design is to rationally design potent therapeutics with multi-targeting effects, higher efficacies, and fewer side effects, especially in terms of toxicity. Methods A wide literature search was performed for writing this review. An updated view on different types of NDs, their effect on human population and a brief introduction to CADD, various approaches involved in this technique, ranging from structural-based to ligand-based drug design has been discussed. The successful application of CADD approaches for the treatment of neurodegenerative disorders is also included in this review. Results In this review, we have briefly described about CADD and its use in the development of the therapeutic drug candidates against NDs. The successful applications, limitations and future prospects of this approach have also been discussed. Conclusion CADD can assist researchers studying interactions between drugs and receptors. We believe this review will be helpful for better understanding of CADD and its applications towards the discovery of new drug candidates against various fatal NDs.
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Affiliation(s)
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Gulam Rabbani
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Mohd Danishuddin
- School of computation and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
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19
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Baqi Y, Pillaiyar T, Abdelrahman A, Kaufmann O, Alshaibani S, Rafehi M, Ghasimi S, Akkari R, Ritter K, Simon K, Spinrath A, Kostenis E, Zhao Q, Köse M, Namasivayam V, Müller CE. 3-(2-Carboxyethyl)indole-2-carboxylic Acid Derivatives: Structural Requirements and Properties of Potent Agonists of the Orphan G Protein-Coupled Receptor GPR17. J Med Chem 2018; 61:8136-8154. [PMID: 30048589 DOI: 10.1021/acs.jmedchem.7b01768] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The orphan receptor GPR17 may be a novel drug target for inflammatory diseases. 3-(2-Carboxyethyl)-4,6-dichloro-1 H-indole-2-carboxylic acid (MDL29,951, 1) was previously identified as a moderately potent GPR17 agonist. In the present study, we investigated the structure-activity relationships (SARs) of 1. Substitution of the indole 1-, 5-, or 7-position was detrimental. Only small substituents were tolerated in the 4-position while the 6-position accommodated large lipophilic residues. Among the most potent compounds were 3-(2-carboxyethyl)-1 H-indole-2-carboxylic acid derivatives containing the following substituents: 6-phenoxy (26, PSB-1737, EC50 270 nM), 4-fluoro-6-bromo (33, PSB-18422, EC50 27.9 nM), 4-fluoro-6-iodo (35, PSB-18484, EC50 32.1 nM), and 4-chloro-6-hexyloxy (43, PSB-1767, EC50 67.0 nM). (3-(2-Carboxyethyl)-6-hexyloxy-1 H-indole-2-carboxylic acid (39, PSB-17183, EC50 115 nM) behaved as a partial agonist. Selected potent compounds tested at human P2Y receptor subtypes showed high selectivity for GPR17. Docking into a homology model of the human GPR17 and molecular dynamic simulation studies rationalized the observed SARs.
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Affiliation(s)
- Younis Baqi
- Department of Chemistry, Faculty of Science , Sultan Qaboos University , P.O. Box 36, 123 Muscat , Oman
| | - Thanigaimalai Pillaiyar
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Aliaa Abdelrahman
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Olesja Kaufmann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Samer Alshaibani
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Saman Ghasimi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Rhalid Akkari
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Kirsten Ritter
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Katharina Simon
- Institute of Pharmaceutical Biology, Section Molecular-, Cellular-, and Pharmacobiology, University of Bonn , Nußallee 6 , 53115 Bonn , Germany
| | - Andreas Spinrath
- Institute of Pharmaceutical Biology, Section Molecular-, Cellular-, and Pharmacobiology, University of Bonn , Nußallee 6 , 53115 Bonn , Germany
| | - Evi Kostenis
- Institute of Pharmaceutical Biology, Section Molecular-, Cellular-, and Pharmacobiology, University of Bonn , Nußallee 6 , 53115 Bonn , Germany
| | - Qiang Zhao
- CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Pudong , Shanghai 201203 , China
| | - Meryem Köse
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany
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20
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Fumagalli M, Lecca D, Coppolino GT, Parravicini C, Abbracchio MP. Pharmacological Properties and Biological Functions of the GPR17 Receptor, a Potential Target for Neuro-Regenerative Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1051:169-192. [PMID: 28828731 DOI: 10.1007/5584_2017_92] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In 2006, cells heterologously expressing the "orphan" receptor GPR17 were shown to acquire responses to both uracil nucleotides and cysteinyl-leukotrienes, two families of signaling molecules accumulating in brain or heart as a result of hypoxic/traumatic injuries. In subsequent years, evidence of GPR17 key role in oligodendrogenesis and myelination has highlighted it as a "model receptor" for new therapies in demyelinating and neurodegenerative diseases. The apparently contrasting evidence in the literature about the role of GPR17 in promoting or inhibiting myelination can be due to its transient expression in the intermediate stages of differentiation, exerting a pro-differentiating function in early oligodendrocyte precursor cells (OPCs), and an inhibitory role in late stage maturing cells. Meanwhile, several papers extended the initial data on GPR17 pharmacology, highlighting a "promiscuous" behavior of this receptor; indeed, GPR17 is able to respond to other emergency signals like oxysterols or the pro-inflammatory cytokine SDF-1, underlying GPR17 ability to adapt its responses to changes of the surrounding extracellular milieu, including damage conditions. Here, we analyze the available literature on GPR17, in an attempt to summarize its emerging biological roles and pharmacological properties.
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Affiliation(s)
- Marta Fumagalli
- Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Davide Lecca
- Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Giusy T Coppolino
- Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Chiara Parravicini
- Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - Maria P Abbracchio
- Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy.
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Abstract
Despite tremendous efforts, approximately 120 GPCRs remain orphan. Their physiological functions and their potential roles in diseases are poorly understood. Orphan GPCRs are extremely important because they may provide novel therapeutic targets for unmet medical needs. As a complement to experimental approaches, molecular modeling and virtual screening are efficient techniques to discover synthetic surrogate ligands which can help to elucidate the role of oGPCRs. Constitutively activated mutants and recently published active structures of GPCRs provide stimulating opportunities for building active molecular models for oGPCRs and identifying activators using virtual screening of compound libraries. We describe the molecular modeling and virtual screening process we have applied in the discovery of surrogate ligands, and provide examples for CCKA, a simulated oGPCR, and for two oGPCRs, GPR52 and GPR34.
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Affiliation(s)
- Constantino Diaz
- Research Informatics, Evotec (France) SAS, 195 Route d'Espagne, 31036, Toulouse, France.
| | | | - Emilie Pihan
- Research Informatics, Evotec (France) SAS, 195 Route d'Espagne, 31036, Toulouse, France
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22
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Identification of small molecules uncoupling the Notch::Jagged interaction through an integrated high-throughput screening. PLoS One 2017; 12:e0182640. [PMID: 29099834 PMCID: PMC5669421 DOI: 10.1371/journal.pone.0182640] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/22/2017] [Indexed: 01/01/2023] Open
Abstract
Notch signaling plays an important role in several cellular functions including growth, differentiation, cell fate determination and stemness. Increased Notch activity has been linked to several types of cancers. Activation of Notch signaling is triggered by the interaction of Notch receptors (Notch1-4) with 5 different ligands (Jagged1-2 and Dll1-3-4) expressed on the neighbouring cells. Currently, indirect approaches to inhibit Notch signalling are based on the inhibition of the key step of Notch activation catalyzed by the γ-Secretase and thereby affect several different γ-Secretase substrates; conversely direct strategies get advantage of antibody-based drugs. The evidence that Jagged-mediated Notch activation plays a key role in cancer cell biology and the interplay with the surrounding microenvironment prompted us to develop a strategy to directly inhibit Notch activation by uncoupling its interaction with the Jagged, using an unprecedented approach based on small molecules. We set-up a screening strategy based on: protein::protein docking of crystallographic structures of Notch1 with Jagged1; comparative modelling of the Notch2:Jagged2 complex, based on the Notch1::Jagged1 complex; in silico high-throughput screening directed to Notch2 interaction surface of a virtual chemical library containing a large variety of molecules commercially available. The predicted pharmacological activity of the selected compounds was validated in vitro by a gene reporter and a viability assay. This approach led to the successful identification of two candidates with different anti-proliferative potency and efficacy. This represents the first step towards the rational identification of candidate molecules for the development of entirely novel drugs directed to inhibit Notch signaling in cancer.
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23
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Saravanan KM, Palanivel S, Yli-Harja O, Kandhavelu M. Identification of novel GPR17-agonists by structural bioinformatics and signaling activation. Int J Biol Macromol 2017; 106:901-907. [PMID: 28827203 DOI: 10.1016/j.ijbiomac.2017.08.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 11/28/2022]
Abstract
G Protein-coupled Receptor 17 (GPR17) is phylogenetically related to the purinergic receptors emerged as a potential drug target for multiple sclerosis, Parkinson disease, Alzheimer disease and cancer. Unfortunately, the crystal structure of GPR17 is unresolved. With the interest in structure-based ligand discovery, we modeled the structure of GPR17. The model allowed us to identify two novel agonists, AC1MLNKK and T0510.3657 that selectively activate GPR17 which exhibit better interaction properties than previously known ligand, MDL29951. We report detailed protein-ligand interactions and the dynamics of GPR17-ligand interaction by molecular docking and molecular dynamics experiments. Ex vivo validation of GPR17-ligand interaction provides evidence that ligand T0510-3657 and AC1MLNKK inhibit the cAMP levels in GPR17-HEK293T cells, with a pEC50 of 4.79 and 4.64, respectively. In silico and ex vivo validation experiments provided the deep understanding of ligand binding with GPR17 and the present findings reported here may lead to use these two compounds as a potential activator of GPR17 for therapeutic intervention.
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Affiliation(s)
- Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Chennai, 600 025, India
| | - Suresh Palanivel
- Molecular Signaling Lab, Computational Systems Biology Research Group, Signal Processing Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland
| | - Olli Yli-Harja
- Molecular Signaling Lab, Computational Systems Biology Research Group, Signal Processing Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USA
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Computational Systems Biology Research Group, Signal Processing Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland.
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24
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Buoso E, Galasso M, Ronfani M, Papale A, Galbiati V, Eberini I, Marinovich M, Racchi M, Corsini E. The scaffold protein RACK1 is a target of endocrine disrupting chemicals (EDCs) with important implication in immunity. Toxicol Appl Pharmacol 2017; 325:37-47. [DOI: 10.1016/j.taap.2017.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 02/02/2023]
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25
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Cordomí A, Fourmy D, Tikhonova IG. Gut hormone GPCRs: structure, function, drug discovery. Curr Opin Pharmacol 2016; 31:63-67. [DOI: 10.1016/j.coph.2016.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/24/2016] [Accepted: 09/01/2016] [Indexed: 01/08/2023]
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26
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Marucci G, Dal Ben D, Lambertucci C, Santinelli C, Spinaci A, Thomas A, Volpini R, Buccioni M. The G Protein-Coupled Receptor GPR17: Overview and Update. ChemMedChem 2016; 11:2567-2574. [PMID: 27863043 DOI: 10.1002/cmdc.201600453] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/17/2016] [Indexed: 11/08/2022]
Abstract
The GPR17 receptor is a G protein-coupled receptor (GPCR) that seems to respond to two unrelated families of endogenous ligands: nucleotide sugars (UDP, UDP-galactose, and UDP-glucose) and cysteinyl leukotrienes (LTD4 , LTC4 , and LTE4 ), with significant affinity at micromolar and nanomolar concentrations, respectively. This receptor has a broad distribution at the level of the central nervous system (CNS) and is found in neurons and in a subset of oligodendrocyte precursor cells (OPCs). Unfortunately, disparate results emerging from different laboratories have resulted in a lack of clarity with regard to the role of GPR17-targeting ligands in OPC differentiation and in myelination. GPR17 is also highly expressed in organs typically undergoing ischemic damage and has various roles in specific phases of adaptations that follow a stroke. Under such conditions, GPR17 plays a crucial role; in fact, its inhibition decreases the progression of ischemic damage. This review summarizes some important features of this receptor that could be a novel therapeutic target for the treatment of demyelinating diseases and for repairing traumatic injury.
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Affiliation(s)
- Gabriella Marucci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Diego Dal Ben
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Catia Lambertucci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Claudia Santinelli
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Andrea Spinaci
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Ajiroghene Thomas
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Rosaria Volpini
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
| | - Michela Buccioni
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino, 1, 62032, Camerino, MC, Italy
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27
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Ngo T, Kufareva I, Coleman JL, Graham RM, Abagyan R, Smith NJ. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol 2016; 173:2934-51. [PMID: 26837045 PMCID: PMC5341249 DOI: 10.1111/bph.13452] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 11/18/2015] [Accepted: 01/29/2016] [Indexed: 12/26/2022] Open
Abstract
GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.
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Affiliation(s)
- Tony Ngo
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - James Lj Coleman
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Robert M Graham
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Nicola J Smith
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
- St. Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, Australia.
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28
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Yanai T, Kurosawa A, Nikaido Y, Nakajima N, Saito T, Osada H, Konno A, Hirai H, Takeda S. Identification and molecular docking studies for novel inverse agonists of SREB, super conserved receptor expressed in brain. Genes Cells 2016; 21:717-27. [PMID: 27184081 DOI: 10.1111/gtc.12378] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/18/2016] [Indexed: 11/28/2022]
Abstract
The identification of novel synthetic ligands for G protein-coupled receptors (GPCRs) is important not only for understanding human physiology, but also for the development of novel drugs, especially for orphan GPCRs for which endogenous ligands are unknown. One of the orphan GPCR subfamilies, Super conserved Receptor Expressed in Brain (SREB), consists of GPR27, GPR85 and GPR173 and is expressed in the central nervous system. We report herein the identification of inverse agonists for the SREB family without their agonists. We carried out an in vitro screening of 5472 chemical compounds from the RIKEN NPDepo chemical library. The binding of [(35) S]GTPγS to the GPR173-Gsα fusion protein expressed in Sf9 cells was measured and resulted in the identification of 8 novel GPR173 inverse agonists. The most potent compound showed an IC50 of approximately 8 μm. The identified compounds were also antagonists for other SREB members, GPR27 and GPR85. These results indicated that the SREB family could couple Gs-type G proteins, and SREB-Gsα fusion proteins showed significant constitutive activities. Moreover, a molecular model of GPR173 was constructed using the screening results. The combination of computational and biological methods will provide a unique approach to ligand identification for orphan GPCRs and brain research.
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Affiliation(s)
- Toshihiro Yanai
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Aya Kurosawa
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Yoshiaki Nikaido
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Nozomi Nakajima
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Tamio Saito
- Collaboration Promotion Unit, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Ayumu Konno
- Department of Neurophysiology and Neural Repair, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Hirokazu Hirai
- Department of Neurophysiology and Neural Repair, Graduate School of Medicine, Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Shigeki Takeda
- Faculty of Science and Technology, Division of Molecular Science, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
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29
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Katsila T, Spyroulias GA, Patrinos GP, Matsoukas MT. Computational approaches in target identification and drug discovery. Comput Struct Biotechnol J 2016; 14:177-84. [PMID: 27293534 PMCID: PMC4887558 DOI: 10.1016/j.csbj.2016.04.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
In the big data era, voluminous datasets are routinely acquired, stored and analyzed with the aim to inform biomedical discoveries and validate hypotheses. No doubt, data volume and diversity have dramatically increased by the advent of new technologies and open data initiatives. Big data are used across the whole drug discovery pipeline from target identification and mechanism of action to identification of novel leads and drug candidates. Such methods are depicted and discussed, with the aim to provide a general view of computational tools and databases available. We feel that big data leveraging needs to be cost-effective and focus on personalized medicine. For this, we propose the interplay of information technologies and (chemo)informatic tools on the basis of their synergy.
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Affiliation(s)
- Theodora Katsila
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - Georgios A. Spyroulias
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Minos-Timotheos Matsoukas
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
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30
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31
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Parravicini C, Daniele S, Palazzolo L, Trincavelli ML, Martini C, Zaratin P, Primi R, Coppolino G, Gianazza E, Abbracchio MP, Eberini I. A promiscuous recognition mechanism between GPR17 and SDF-1: Molecular insights. Cell Signal 2016; 28:631-42. [PMID: 26971834 DOI: 10.1016/j.cellsig.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 01/19/2023]
Abstract
Recent data and publications suggest a promiscuous behaviour for GPR17, a class-A GPCR operated by different classes of ligands, such as uracil nucleotides, cysteinyl-leukotrienes and oxysterols. This observation, together with the ability of several class-A GPCRs to form homo- and hetero-dimers, is likely to unveil new pathophysiological roles and novel emerging pharmacological properties for some of these GPCRs, including GPR17. This receptor shares structural, phylogenetic and functional properties with some chemokine receptors, CXCRs. Both GPR17 and CXCR2 are operated by oxysterols, and both GPR17 and CXCR ligands have been demonstrated to have a role in orchestrating inflammatory responses and oligodendrocyte precursor cell differentiation to myelinating cells in acute and chronic diseases of the central nervous system. Here, by combining in silico modelling data with in vitro validation in (i) a classical reference pharmacological assay for GPCR activity and (ii) a model of maturation of primary oligodendrocyte precursor cells, we demonstrate that GPR17 can be activated by SDF-1, a ligand of chemokine receptors CXCR4 and CXCR7, and investigate the underlying molecular recognition mechanism. We also demonstrate that cangrelor, a GPR17 orthosteric antagonist, can block the SDF-1-mediated activation of GPR17 in a concentration-dependent manner. The ability of GPR17 to respond to different classes of GPCR ligands suggests that this receptor modifies its function depending on the extracellular mileu changes occurring under specific pathophysiological conditions and advocates it as a strategic target for neurodegenerative diseases with an inflammatory/immune component.
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Affiliation(s)
- Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Simona Daniele
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | | | - Claudia Martini
- Dipartimento di Farmacia, Università degli Studi di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
| | - Paola Zaratin
- Fondazione Italiana Sclerosi Multipla, Via Operai 40, 16149 Genova, Italy.
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Giusy Coppolino
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Maria P Abbracchio
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy; Dipartimento di Scienze Biomediche e Cliniche "L. Sacco", Università degli Studi di Milano, Via Gian Battista Grassi 74, 20157 Milano, Italy.
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32
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Molecular mechanisms of target recognition by lipid GPCRs: relevance for cancer. Oncogene 2015; 35:4021-35. [DOI: 10.1038/onc.2015.467] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/02/2015] [Accepted: 11/02/2015] [Indexed: 12/18/2022]
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33
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Viganò F, Schneider S, Cimino M, Bonfanti E, Gelosa P, Sironi L, Abbracchio MP, Dimou L. GPR17 expressing NG2-Glia: Oligodendrocyte progenitors serving as a reserve pool after injury. Glia 2015; 64:287-99. [PMID: 26464068 DOI: 10.1002/glia.22929] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 11/07/2022]
Abstract
In the adult brain NG2-glia continuously generate mature, myelinating oligodendrocytes. To which extent the differentiation process is common to all NG2-glia and whether distinct pools are recruited for repair under physiological and pathological conditions still needs clarification. Here, we aimed at investigating the differentiation potential of adult NG2-glia that specifically express the G-protein coupled receptor 17 (GPR17), a membrane receptor that regulates the differentiation of these cells at postnatal stages. To this aim, we generated the first BAC transgenic GPR17-iCreER(T2) mouse line for fate mapping studies. In these mice, under physiological conditions, GPR17(+) cells--in contrast to GPR17(-) NG2-glia--did not differentiate within 3 months, a peculiarity that was overcome after cerebral damage induced by acute injury or ischemia. After these insults, GPR17(+) NG2-glia rapidly reacted to the damage and underwent maturation, suggesting that they represent a 'reserve pool' of adult progenitors maintained for repair purposes.
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Affiliation(s)
- Francesca Viganò
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, 80336, Germany.,Helmholtz Zentrum Munich, Institute for Stem Cell Research, Neuherberg, 85764, Germany
| | - Sarah Schneider
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, 80336, Germany
| | - Mauro Cimino
- Department of Biomolecular Sciences, University of Urbino, Urbino, 61029, Italy
| | - Elisabetta Bonfanti
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Paolo Gelosa
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy.,Centro Cardiologico Monzino, Milan, 20138, Italy
| | - Luigi Sironi
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy.,Centro Cardiologico Monzino, Milan, 20138, Italy
| | - Maria P Abbracchio
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Leda Dimou
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, 80336, Germany.,Helmholtz Zentrum Munich, Institute for Stem Cell Research, Neuherberg, 85764, Germany.,SYNERGY, Excellence Cluster of Systemic Neurology, Ludwig-Maximilians-University, Munich, 81377, Germany
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34
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CNS remyelination as a novel reparative approach to neurodegenerative diseases: The roles of purinergic signaling and the P2Y-like receptor GPR17. Neuropharmacology 2015; 104:82-93. [PMID: 26453964 DOI: 10.1016/j.neuropharm.2015.10.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/02/2015] [Accepted: 10/03/2015] [Indexed: 02/07/2023]
Abstract
Oligodendrocytes are the myelin-forming cells in the CNS. They enwrap axons, thus permitting fast impulse transmission and exerting trophic actions on neurons. Demyelination accompanied by neurological deficit is a rather frequent condition that is not only associated with multiple sclerosis but has been also recognized in several other neurodegenerative diseases, including brain trauma and stroke, Alzheimer's disease and amyotrophic lateral sclerosis. Recently, alterations of myelin function have been also reported in neuropsychiatric diseases, like depression and autism. Highly relevant for therapeutic purposes, oligodendrocyte precursor cells (OPCs) still persist in the adult brain and spinal cord. These cells are normally rather quiescent, but under specific circumstances, they can be stimulated to undergo differentiation and generate mature myelinating oligodendrocytes. Thus, approaches aimed at restoring myelin integrity and at fostering a correct oligodendrocyte function are now viewed as novel therapeutic opportunities for both neurodegenerative and neuropsychiatric diseases. Both OPCs and mature oligodendrocytes express purinergic receptors. For some of these receptors, expression is restricted at specific differentiation stages, suggesting key roles in OPCs maturation and myelination. Some of these receptors are altered under demyelinating conditions, suggesting that their dysregulation may contribute to disease development and could represent adequate new targets for remyelinating therapies. Here, we shall describe the current literature available on all these receptors, with special emphasis on the P2Y-like GPR17 receptor, that represents one of the most studied receptor subtypes in these cells. This article is part of the Special Issue entitled 'Purines in Neurodegeneration and Neuroregeneration'.
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Key Words
- 2′-Deoxy-N(6)-methyladenosine 3′,5'-bisphosphate ammonium salt (MRS2179)
- 3-(2-carboxy-4,6-dichloro-indol-3-yl)propionic acid (MDL29,951)
- 3-[4-[2-[ [6-amino-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]purin-2-yl]amino]ethyl]phenyl]propanoic acid (CGS21680)
- 7-(2-phenylethyl)-5-amino-2-(2-furyl)-pyrazolo-[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine (SCH58261)
- ADP
- ATP
- Adenosine
- Brilliant blue G (BBG)
- Leukotriene D4 (LTD(4))
- Montelukast
- N6-cyclohexyladenosine (CHA)
- Oligodendrocytes
- Oxidized ATP (oxATP)
- Purinergic receptors
- Rapamycin
- Remyelination
- UDP
- UDP-Glucose
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35
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Stockert JA, Devi LA. Advancements in therapeutically targeting orphan GPCRs. Front Pharmacol 2015; 6:100. [PMID: 26005419 PMCID: PMC4424851 DOI: 10.3389/fphar.2015.00100] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/21/2015] [Indexed: 11/23/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are popular biological targets for drug discovery and development. To date there are more than 140 orphan GPCRs, i.e., receptors whose endogenous ligands are unknown. Traditionally orphan GPCRs have been difficult to study and the development of therapeutic compounds targeting these receptors has been extremely slow although these GPCRs are considered important targets based on their distribution and behavioral phenotype as revealed by animals lacking the receptor. Recent advances in several methods used to study orphan receptors, including protein crystallography and homology modeling are likely to be useful in the identification of therapeutics targeting these receptors. In the past 13 years, over a dozen different Class A GPCRs have been crystallized; this trend is exciting, since homology modeling of GPCRs has previously been limited by the availability of solved structures. As the number of solved GPCR structures continues to grow so does the number of templates that can be used to generate increasingly accurate models of phylogenetically related orphan GPCRs. The availability of solved structures along with the advances in using multiple templates to build models (in combination with molecular dynamics simulations that reveal structural information not provided by crystallographic data and methods for modeling hard-to-predict flexible loop regions) have improved the quality of GPCR homology models. This, in turn, has improved the success rates of virtual ligand screens that use homology models to identify potential receptor binding compounds. Experimental testing of the predicted hits and validation using traditional GPCR pharmacological approaches can be used to drive ligand-based efforts to probe orphan receptor biology as well as to define the chemotypes and chemical scaffolds important for binding. As a result of these advances, orphan GPCRs are emerging from relative obscurity as a new class of drug targets.
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Affiliation(s)
- Jennifer A Stockert
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Lakshmi A Devi
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY USA
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Ahmad R, Wojciech S, Jockers R. Hunting for the function of orphan GPCRs - beyond the search for the endogenous ligand. Br J Pharmacol 2014; 172:3212-28. [PMID: 25231237 DOI: 10.1111/bph.12942] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/04/2014] [Accepted: 09/09/2014] [Indexed: 12/13/2022] Open
Abstract
Seven transmembrane-spanning proteins (7TM), also called GPCRs, are among the most versatile and evolutionary successful protein families. Out of the 400 non-odourant members identified in the human genome, approximately 100 remain orphans that have not been matched with an endogenous ligand. Apart from the classical deorphanization strategies, several alternative strategies provided recent new insights into the function of these proteins, which hold promise for high therapeutic potential. These alternative strategies consist of the phenotypical characterization of organisms silenced or overexpressing orphan 7TM proteins, the search for constitutive receptor activity and formation of protein complexes including 7TM proteins as well as the development of synthetic, surrogate ligands. Taken together, a variety of ligand-independent functions can be attributed to orphan 7TM proteins that range from constitutive activity to complex formation with other proteins and include 'true' orphans for which no ligand exist and 'conditional' orphans that behave like orphans in the absence of ligand and as non-orphans in the presence of ligand.
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Affiliation(s)
- Raise Ahmad
- Institut Cochin, INSERM, Paris, France.,CNRS UMR 8104, Paris, France.,Paris Descartes University, Paris, France
| | - Stefanie Wojciech
- Institut Cochin, INSERM, Paris, France.,CNRS UMR 8104, Paris, France.,Paris Descartes University, Paris, France
| | - Ralf Jockers
- Institut Cochin, INSERM, Paris, France.,CNRS UMR 8104, Paris, France.,Paris Descartes University, Paris, France
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Oxysterols act as promiscuous ligands of class-A GPCRs: In silico molecular modeling and in vitro validation. Cell Signal 2014; 26:2614-20. [DOI: 10.1016/j.cellsig.2014.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/15/2014] [Indexed: 01/12/2023]
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Zaratin P, Battaglia MA, Abbracchio MP. Nonprofit foundations spur translational research. Trends Pharmacol Sci 2014; 35:552-5. [DOI: 10.1016/j.tips.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/02/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023]
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Galli CL, Sensi C, Fumagalli A, Parravicini C, Marinovich M, Eberini I. A computational approach to evaluate the androgenic affinity of iprodione, procymidone, vinclozolin and their metabolites. PLoS One 2014; 9:e104822. [PMID: 25111804 PMCID: PMC4128724 DOI: 10.1371/journal.pone.0104822] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/17/2014] [Indexed: 11/18/2022] Open
Abstract
Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking. Three different classes of molecules with well-known endocrine activity (iprodione, procymidone, vinclozolin, and a selection of their metabolites) were evaluated. Our approach was demonstrated useful as the first step of chemical safety evaluation since ligand-target interaction is a necessary condition for exerting any biological effect. Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three). This evidence suggests that, in order not to over-/under-estimate the risks connected with the use of a chemical entity, further in vitro and/or in vivo tests should be carried out only after an accurate evaluation of the most suitable cellular system or animal species. The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.
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Affiliation(s)
- Corrado Lodovico Galli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Cristina Sensi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Amos Fumagalli
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Marina Marinovich
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
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Sensi C, Simonelli S, Zanotti I, Tedeschi G, Lusardi G, Franceschini G, Calabresi L, Eberini I. Distant homology modeling of LCAT and its validation through in silico targeting and in vitro and in vivo assays. PLoS One 2014; 9:e95044. [PMID: 24736652 PMCID: PMC3988154 DOI: 10.1371/journal.pone.0095044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/23/2014] [Indexed: 11/18/2022] Open
Abstract
LCAT (lecithin:cholesterol acyltransferase) catalyzes the transacylation of a fatty acid of lecithin to cholesterol, generating a cholesteryl ester and lysolecithin. The knowledge of LCAT atomic structure and the identification of the amino acids relevant in controlling its structure and function are expected to be very helpful to understand the enzyme catalytic mechanism, as involved in HDL cholesterol metabolism. However - after an early report in the late ‘90 s - no recent advance has been made about LCAT three-dimensional structure. In this paper, we propose an LCAT atomistic model, built following the most up-to-date molecular modeling approaches, and exploiting newly solved crystallographic structures. LCAT shows the typical folding of the α/β hydrolase superfamily, and its topology is characterized by a combination of α-helices covering a central 7-strand β-sheet. LCAT presents a Ser/Asp/His catalytic triad with a peculiar geometry, which is shared with such other enzyme classes as lipases, proteases and esterases. Our proposed model was validated through different approaches. We evaluated the impact on LCAT structure of some point mutations close to the enzyme active site (Lys218Asn, Thr274Ala, Thr274Ile) and explained, at a molecular level, their phenotypic effects. Furthermore, we devised some LCAT modulators either designed through a de novo strategy or identified through a virtual high-throughput screening pipeline. The tested compounds were proven to be potent inhibitors of the enzyme activity.
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Affiliation(s)
- Cristina Sensi
- Laboratorio di Biochimica e Biofisica Computazionale, Università degli Studi di Milano, Milano, Italia
| | - Sara Simonelli
- Centro Enrica Grossi Paoletti, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Ilaria Zanotti
- Dipartimento di Farmacia, Università Degli Studi di Parma, Parma, Italia
| | - Gabriella Tedeschi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Milano, Italia
| | - Giulia Lusardi
- Dipartimento di Farmacia, Università Degli Studi di Parma, Parma, Italia
| | - Guido Franceschini
- Centro Enrica Grossi Paoletti, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Laura Calabresi
- Centro Enrica Grossi Paoletti, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia
| | - Ivano Eberini
- Laboratorio di Biochimica e Biofisica Computazionale, Università degli Studi di Milano, Milano, Italia
- * E-mail:
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Pochini L, Seidita A, Sensi C, Scalise M, Eberini I, Indiveri C. Nimesulide binding site in the B0AT1 (SLC6A19) amino acid transporter. Mechanism of inhibition revealed by proteoliposome transport assay and molecular modelling. Biochem Pharmacol 2014; 89:422-30. [PMID: 24704252 DOI: 10.1016/j.bcp.2014.03.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 11/29/2022]
Abstract
The effect of pharmaceutical compounds on the rat kidney B0AT1 transporter in proteoliposomes has been screened. To this aim, inhibition of the transport activity by the different compounds was measured on Na(+)-[(3)H]glutamine co-transport in the presence of membrane potential positive outside. Most of the tested drugs had no effect on the transport activity. Some compounds exhibited inhibitory effects from 5 to 88% at concentration of 300μM. Among the tested compounds, only the anti-inflammatory drug nimesulide exerted potent inhibition on B0AT1. From dose response analysis, an IC50 value of 23μM was found. Inhibition kinetic analysis was performed: noncompetitive inhibition of the glutamine transport was observed while competitive behaviour was found when the inhibition was analyzed with respect to the Na(+) concentration. Several molecules harbouring functional groups of nimesulide (analogues) were tested as inhibitors. None among the tested molecules has the capacity to inhibit the transport with the exception of the compound NS-398, whose chemical structure is very close to that of whole nimesulide. The IC50 for this compound was 131μM. Inhibition kinetics showed behaviour of NS-398 identical to that of nimesulide, i.e., noncompetitive inhibition respect to glutamine and competitive inhibition respect to Na(+). Molecular docking of nimesulide suggested that this drug is able to bind B0AT1 in an external dedicated binding site and that its binding produces a steric hindrance effect of the protein translocation path abolishing the transporter activity.
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Affiliation(s)
- Lorena Pochini
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Angela Seidita
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Cristina Sensi
- Laboratorio di Biochimica e Biofisica Computazionale, Dipartimento di Scienze Farmacologiche e Biomolecolari Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia Università degli Studi di Milano Via Trentacoste, 22134 Milano, Italy
| | - Mariafrancesca Scalise
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Ivano Eberini
- Laboratorio di Biochimica e Biofisica Computazionale, Dipartimento di Scienze Farmacologiche e Biomolecolari Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia Università degli Studi di Milano Via Trentacoste, 22134 Milano, Italy
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036 Arcavacata di Rende, Italy.
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Hennen S, Wang H, Peters L, Merten N, Simon K, Spinrath A, Blättermann S, Akkari R, Schrage R, Schröder R, Schulz D, Vermeiren C, Zimmermann K, Kehraus S, Drewke C, Pfeifer A, König GM, Mohr K, Gillard M, Müller CE, Lu QR, Gomeza J, Kostenis E. Decoding signaling and function of the orphan G protein-coupled receptor GPR17 with a small-molecule agonist. Sci Signal 2013; 6:ra93. [PMID: 24150254 DOI: 10.1126/scisignal.2004350] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Replacement of the lost myelin sheath is a therapeutic goal for treating demyelinating diseases of the central nervous system (CNS), such as multiple sclerosis (MS). The G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptor (GPCR) GPR17, which is phylogenetically closely related to receptors of the "purinergic cluster," has emerged as a modulator of CNS myelination. However, whether GPR17-mediated signaling positively or negatively regulates this critical process is unresolved. We identified a small-molecule agonist, MDL29,951, that selectively activated GPR17 even in a complex environment of endogenous purinergic receptors in primary oligodendrocytes. MDL29,951-stimulated GPR17 engaged the entire set of intracellular adaptor proteins for GPCRs: G proteins of the Gα(i), Gα(s), and Gα(q) subfamily, as well as β-arrestins. This was visualized as alterations in the concentrations of cyclic adenosine monophosphate and inositol phosphate, increased Ca²⁺ flux, phosphorylation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), as well as multifeatured cell activation recorded with label-free dynamic mass redistribution and impedance biosensors. MDL29,951 inhibited the maturation of primary oligodendrocytes from heterozygous but not GPR17 knockout mice in culture, as well as in cerebellar slices from 4-day-old wild-type mice. Because GPCRs are attractive targets for therapeutic intervention, inhibiting GPR17 emerges as therapeutic strategy to relieve the oligodendrocyte maturation block and promote myelin repair in MS.
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Affiliation(s)
- Stephanie Hennen
- 1Molecular, Cellular, and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, 53115 Bonn, Germany
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43
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Present and future approaches to screening of G-protein-coupled receptors. Future Med Chem 2013; 5:523-38. [PMID: 23573971 DOI: 10.4155/fmc.13.9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
As G-protein-coupled receptors (GPCRs) mediate a multitude of cellular signal transduction events, affecting more or less all human disease areas, it is, therefore, no surprise that they comprise the largest family of current drug targets. Screening of compounds interacting with GPCRs has developed during the past decade from receptor binding assays, to various functional determination of coupling to G-proteins, and, more recently, G-protein-independent signal transduction events. Additional opportunities have been presented in drug discovery through novel pharmacological properties obtained for receptor dimers and by identification of ligands for orphan GPCRs. Furthermore, high-throughput formats and automation has substantially facilitated and accelerated the screening process providing powerful tools in improving modern drug discovery.
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Franke H, Parravicini C, Lecca D, Zanier ER, Heine C, Bremicker K, Fumagalli M, Rosa P, Longhi L, Stocchetti N, De Simoni MG, Weber M, Abbracchio MP. Changes of the GPR17 receptor, a new target for neurorepair, in neurons and glial cells in patients with traumatic brain injury. Purinergic Signal 2013; 9:451-62. [PMID: 23801362 PMCID: PMC3757149 DOI: 10.1007/s11302-013-9366-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/09/2013] [Indexed: 11/29/2022] Open
Abstract
Unveiling the mechanisms participating in the damage and repair of traumatic brain injury (TBI) is fundamental to develop new therapies. The P2Y-like GPR17 receptor has recently emerged as a sensor of damage and a key actor in lesion remodeling/repair in the rodent brain, but its role in humans is totally unknown. Here, we characterized GPR17 expression in brain specimens from seven intensive care unit TBI patients undergoing neurosurgery for contusion removal and from 28 autoptic TBI cases (and 10 control subjects of matched age and gender) of two university hospitals. In both neurosurgery and autoptic samples, GPR17 expression was strong inside the contused core and progressively declined distally according to a spatio-temporal gradient. Inside and around the core, GPR17 labeled dying neurons, reactive astrocytes, and activated microglia/macrophages. In peri-contused parenchyma, GPR17 decorated oligodendrocyte precursor cells (OPCs) some of which had proliferated, indicating re-myelination attempts. In autoptic cases, GPR17 expression positively correlated with death for intracranial complications and negatively correlated with patients' post-traumatic survival. Data indicate lesion-specific sequential involvement of GPR17 in the (a) death of irreversibly damaged neurons, (b) activation of microglia/macrophages remodeling the lesion, and (c) activation/proliferation of multipotent parenchymal progenitors (both reactive astrocytes and OPCs) starting repair processes. Data validate GPR17 as a target for neurorepair and are particularly relevant to setting up new therapies for TBI patients.
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Affiliation(s)
- Heike Franke
- />Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Leipzig, Germany
| | - Chiara Parravicini
- />Department of Pharmacological and Biomolecular Sciences, Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, University of Milan, via Balzaretti 9, 20133 Milan, Italy
| | - Davide Lecca
- />Department of Pharmacological and Biomolecular Sciences, Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, University of Milan, via Balzaretti 9, 20133 Milan, Italy
| | - Elisa R. Zanier
- />IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy
| | - Claudia Heine
- />Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Leipzig, Germany
- />Translational Centre for Regenerative Medicine (TRM), University of Leipzig, Leipzig, Germany
| | - Kristina Bremicker
- />Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Leipzig, Germany
| | - Marta Fumagalli
- />Department of Pharmacological and Biomolecular Sciences, Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, University of Milan, via Balzaretti 9, 20133 Milan, Italy
| | - Patrizia Rosa
- />Department of Medical Pharmacology, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Luca Longhi
- />Department of Pathophysiology and Transplantation, University of Milan, and Neurosurgical Care Unit, IRCCS Ca’ Granda - Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Nino Stocchetti
- />Department of Pathophysiology and Transplantation, University of Milan, and Neurosurgical Care Unit, IRCCS Ca’ Granda - Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | | | - Marco Weber
- />Institute of Legal Medicine, University of Halle, Halle (Saale), Germany
| | - Maria P. Abbracchio
- />Department of Pharmacological and Biomolecular Sciences, Laboratory of Molecular and Cellular Pharmacology of Purinergic Transmission, University of Milan, via Balzaretti 9, 20133 Milan, Italy
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Structure-based drug design using GPCR homology modeling: toward the discovery of novel selective CysLT2 antagonists. Eur J Med Chem 2013; 62:754-63. [PMID: 23455026 DOI: 10.1016/j.ejmech.2013.01.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/16/2013] [Accepted: 01/24/2013] [Indexed: 12/31/2022]
Abstract
3D structure of CysLT2 receptor was constructed by using homology modeling and molecular simulations. The binding pocket of CysLT2 receptor and the proposition of the interaction mode between CysLT2 and HAMI3379 were identified. A series of dicarboxylated chalcones was then virtually evaluated through molecular docking studies. A total of six compounds 13a-f with preferable scores was further synthesized and tested for CysLT2 antagonistic activities by determination of the cytosolic free Ca(2+) levels in HEK293 cells. Compounds 13e and 13f exhibited potent and selective CysLT2 antagonistic activities with IC50 values being 7.5 and 0.25 μM, respectively.
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Seddon G, Lounnas V, McGuire R, van den Bergh T, Bywater RP, Oliveira L, Vriend G. Drug design for ever, from hype to hope. J Comput Aided Mol Des 2012; 26:137-50. [PMID: 22252446 PMCID: PMC3268973 DOI: 10.1007/s10822-011-9519-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/05/2011] [Indexed: 01/28/2023]
Abstract
In its first 25 years JCAMD has been disseminating a large number of techniques aimed at finding better medicines faster. These include genetic algorithms, COMFA, QSAR, structure based techniques, homology modelling, high throughput screening, combichem, and dozens more that were a hype in their time and that now are just a useful addition to the drug-designers toolbox. Despite massive efforts throughout academic and industrial drug design research departments, the number of FDA-approved new molecular entities per year stagnates, and the pharmaceutical industry is reorganising accordingly. The recent spate of industrial consolidations and the concomitant move towards outsourcing of research activities requires better integration of all activities along the chain from bench to bedside. The next 25 years will undoubtedly show a series of translational science activities that are aimed at a better communication between all parties involved, from quantum chemistry to bedside and from academia to industry. This will above all include understanding the underlying biological problem and optimal use of all available data.
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Affiliation(s)
- G Seddon
- Adelard Institute, Manchester, UK
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47
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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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