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Farajzadeh-Dehkordi M, Mafakher L, Harifi A, Haghdoost-Yazdi H, Piri H, Rahmani B. Unraveling the function and structure impact of deleterious missense SNPs in the human OX1R receptor by computational analysis. Sci Rep 2024; 14:833. [PMID: 38191899 PMCID: PMC10774445 DOI: 10.1038/s41598-023-49809-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
The orexin/hypocretin receptor type 1 (OX1R) plays a crucial role in regulating various physiological functions, especially feeding behavior, addiction, and reward. Genetic variations in the OX1R have been associated with several neurological disorders. In this study, we utilized a combination of sequence and structure-based computational tools to identify the most deleterious missense single nucleotide polymorphisms (SNPs) in the OX1R gene. Our findings revealed four highly conserved and structurally destabilizing missense SNPs, namely R144C, I148N, S172W, and A297D, located in the GTP-binding domain. Molecular dynamics simulations analysis demonstrated that all four most detrimental mutant proteins altered the overall structural flexibility and dynamics of OX1R protein, resulting in significant changes in the structural organization and motion of the protein. These findings provide valuable insights into the impact of missense SNPs on OX1R function loss and their potential contribution to the development of neurological disorders, thereby guiding future research in this field.
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Affiliation(s)
- Mahvash Farajzadeh-Dehkordi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abbas Harifi
- Department of Electrical and Computer Engineering, University of Hormozgan, Bandar Abbas, Hormozgan, Iran
| | - Hashem Haghdoost-Yazdi
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hossein Piri
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Babak Rahmani
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran.
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2
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Couvineau A, Nicole P, Gratio V, Voisin T. The Orexin receptors: Structural and anti-tumoral properties. Front Endocrinol (Lausanne) 2022; 13:931970. [PMID: 35966051 PMCID: PMC9365956 DOI: 10.3389/fendo.2022.931970] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022] Open
Abstract
At the end of the 20th century, two new neuropeptides (Orexin-A/hypocretin-1 and Orexin-B/hypocretins-2) expressed in hypothalamus as a prepro-orexins precursor, were discovered. These two neuropeptides interacted with two G protein-coupled receptor isoforms named OX1R and OX2R. The orexins/OX receptors system play an important role in the central and peripheral nervous system where it controls wakefulness, addiction, reward seeking, stress, motivation, memory, energy homeostasis, food intake, blood pressure, hormone secretions, reproduction, gut motility and lipolysis. Orexins and their receptors are involved in pathologies including narcolepsy type I, neuro- and chronic inflammation, neurodegenerative diseases, metabolic syndrome, and cancers. Associated with these physiopathological roles, the extensive development of pharmacological molecules including OXR antagonists, has emerged in association with the determination of the structural properties of orexins and their receptors. Moreover, the identification of OX1R expression in digestive cancers encompassing colon, pancreas and liver cancers and its ability to trigger mitochondrial apoptosis in tumoral cells, indicate a new putative therapeutical action of orexins and paradoxically OXR antagonists. The present review focuses on structural and anti-tumoral aspects of orexins and their receptors.
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3
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Lessel U, Ferrara M, Heine N, Marelli C, Carrettoni L, Pfau R, Schmidt E, Riether D. Identification of Highly Selective Orexin 1 Receptor Antagonists Driven by Structure-Based Design. J Chem Inf Model 2021; 61:5893-5905. [PMID: 34817173 DOI: 10.1021/acs.jcim.1c01055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OX1 receptor antagonists are of interest to treat, for example, substance abuse disorders, personality disorders, eating disorders, or anxiety-related disorders. However, known dual OX1/OX2 receptor antagonists are not suitable due to their sleep-inducing effects; therefore, we were interested in identifying a highly OX1 selective antagonist with a sufficient window to OX2-mediated effects. Herein, we describe the design of highly selective OX1 receptor antagonists driven by the X-ray structure of OX1 with suvorexant, a dual OX1/OX2 receptor antagonist. Moderately selective OX1 antagonists comprising a [2.2.1]-bicyclic scaffold served as our starting point. Based on our binding mode hypothesis, we postulated which part of the scaffold points toward one of the regions where the two binding pockets differ. Structural changes in this part resulted in a modified core with higher inherent selectivity compared to the [2.2.1]-bicyclic template. The structure-based design, synthesis, and hit-to-lead evaluation of this novel OX1 receptor-selective scaffold are discussed herein.
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Affiliation(s)
- Uta Lessel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Marco Ferrara
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Niklas Heine
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Chiara Marelli
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Laura Carrettoni
- Boehringer Ingelheim Research Italia S.a.s. di BI IT S.r.l., Via Giovanni Lorenzini 8, 20139 Milano, MI, Italy
| | - Roland Pfau
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Esther Schmidt
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany
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4
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Synthesis and biological evaluation of novel 18F-labeled phenylbenzofuran-2-carboxamide derivative for detection of orexin 1 receptor in the brain. Bioorg Med Chem Lett 2021; 43:128098. [PMID: 33984472 DOI: 10.1016/j.bmcl.2021.128098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 01/12/2023]
Abstract
Although the orexin 1 receptor (OX1R) in the brain is considered to regulate reward and feeding, the in vivo function of OX1R has not been fully elucidated. In vivo imaging of OX1R with positron emission tomography (PET) may be useful to further understand the molecular details of OX1R. In this study, we newly designed and synthesized a phenylbenzofuran-2-carboxamide (PBC) derivative ([18F]PBC-1) and evaluated its utility as a PET probe targeting OX1R in the brain. The results of cell binding assays suggested that [18F]PBC-1 has affinity for OX1R. In an in vitro competitive inhibition assay, PBC-1 showed selective binding affinity for OX1R (IC50 = 19.5 nM) over orexin 2 receptor (IC50 = 456.7 nM). Furthermore, [18F]PBC-1 displayed sufficient brain uptake for in vivo imaging with PET in a biodistribution study using normal mice, but in vivo instability was observed. These results suggest that further modifications for improvement of the pharmacokinetics are needed, but the PBC scaffold has potential for the development of useful PET probes targeting OX1R in the brain.
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5
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Sarukhanyan E, Shityakov S, Dandekar T. Rational Drug Design of Axl Tyrosine Kinase Type I Inhibitors as Promising Candidates Against Cancer. Front Chem 2020; 7:920. [PMID: 32117858 PMCID: PMC7010640 DOI: 10.3389/fchem.2019.00920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
The high level of Axl tyrosine kinase expression in various cancer cell lines makes it an attractive target for the development of anti-cancer drugs. In this study, we carried out several sets of in silico screening for the ATP-competitive Axl kinase inhibitors based on different molecular docking protocols. The best drug-like candidates were identified, after parental structure modifications, by their highest affinity to the target protein. We found that our newly designed compound R5, a derivative of the R428 patented analog, is the most promising inhibitor of the Axl kinase according to the three molecular docking algorithms applied in the study. The molecular docking results are in agreement with the molecular dynamics simulations using the MM-PBSA/GBSA implicit solvation models, which confirm the high affinity of R5 toward the protein receptor. Additionally, the selectivity test against other kinases also reveals a high affinity of R5 toward ABL1 and Tyro3 kinases, emphasizing its promising potential for the treatment of malignant tumors.
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Affiliation(s)
- Edita Sarukhanyan
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sergey Shityakov
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Department of Anesthesia and Critical Care, University Hospital Würzburg, Würzburg, Germany.,Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung, Taiwan.,College of Medicine, China Medical University, Taichung, Taiwan
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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7
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Perrey DA, Zhang Y. Therapeutics development for addiction: Orexin-1 receptor antagonists. Brain Res 2018; 1731:145922. [PMID: 30148984 DOI: 10.1016/j.brainres.2018.08.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/12/2022]
Abstract
The orexin system includes the neuropeptides orexin A and B and the cognate receptors of orexin-1 (OX1) and -2 (OX2) and has been indicated in a number of important physiological processes. It is generally accepted that the OX1 receptor is mainly involved in motivation and reward and the OX2 receptor in the modulation of sleep/wake cycle and energy homeostasis. A variety of OX1 selective antagonists (1-SORAs) have been disclosed in the literature and some of them have been evaluated as potential therapeutics for addiction treatment. In this review we summarize all OX1 antagonists reported thus far based on their core structure. Several dual orexin receptor antagonists (DORAs) and OX2 selective antagonist (2-SORAs) have also been recently evaluated in reward and addiction models. While DORAs may seem pharmacologically advantageous for alcohol addiction given the recent findings on the OX2 receptor in reward and alcohol consumption, 1-SORAs are the better options for other drugs of addiction such as cocaine due to the absence of the sedative effects inherently associated with dual antagonists.
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Affiliation(s)
- David A Perrey
- Research Triangle Institute, Research Triangle Park, NC 27709, USA
| | - Yanan Zhang
- Research Triangle Institute, Research Triangle Park, NC 27709, USA.
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8
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Bai Q, Pérez-Sánchez H, Shi Z, Li L, Shi D, Liu H, Yao X. Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations. Chem Biol Drug Des 2018; 92:1221-1231. [PMID: 29450984 DOI: 10.1111/cbdd.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/08/2017] [Accepted: 11/11/2017] [Indexed: 12/29/2022]
Abstract
The FDA approved drug suvorexant binds to the horseshoe shape pocket of OX2 R with the boat conformation. The horseshoe shape pocket plays an important role on the biological activity of OX2 R in the cell membrane. To study the binding mechanism between the horseshoe shape pocket of OX2 R and boat conformation of suvorexant, the crystal structures of wild type and N324A mutant of OX2 R in complex with antagonist suvorexant are chosen to perform molecular dynamics (MD) simulations, QM/MM, and MMGBSA calculations. By comparison with the wild type of OX2 R, the results show the 1,2,3-triazole and p-toluamide groups of suvorexant are changed in the N324A mutant of OX2 R during 200 ns MD simulations. The QM/MM and weak interaction analysis are employed to calculate the non-covalent bonds interaction between suvorexant and key residues in the wild type and N324A mutant of OX2 R. The MMGBSA calculations indicate the entropy energy is an important influence factor for suvorexant affinity in the distorted horseshoe shape pocket of OX2 R. Our results not only show the horseshoe shape pocket of OX2 R is the necessary conformation for the binding of antagonist suvorexant, but also give the important sites and structural features for antagonist design of OX2 R.
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Affiliation(s)
- Qifeng Bai
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Horacio Pérez-Sánchez
- Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Zhuoyu Shi
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Lanlan Li
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
| | - Danfeng Shi
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
| | - Huanxiang Liu
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojun Yao
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China.,Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
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9
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Heifetz A, Southey M, Morao I, Townsend-Nicholson A, Bodkin MJ. Computational Methods Used in Hit-to-Lead and Lead Optimization Stages of Structure-Based Drug Discovery. Methods Mol Biol 2018; 1705:375-394. [PMID: 29188574 DOI: 10.1007/978-1-4939-7465-8_19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GPCR modeling approaches are widely used in the hit-to-lead (H2L) and lead optimization (LO) stages of drug discovery. The aims of these modeling approaches are to predict the 3D structures of the receptor-ligand complexes, to explore the key interactions between the receptor and the ligand and to utilize these insights in the design of new molecules with improved binding, selectivity or other pharmacological properties. In this book chapter, we present a brief survey of key computational approaches integrated with hierarchical GPCR modeling protocol (HGMP) used in hit-to-lead (H2L) and in lead optimization (LO) stages of structure-based drug discovery (SBDD). We outline the differences in modeling strategies used in H2L and LO of SBDD and illustrate how these tools have been applied in three drug discovery projects.
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK. .,Division of Biosciences, Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
| | - Michelle Southey
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Inaki Morao
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Andrea Townsend-Nicholson
- Division of Biosciences, Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Mike J Bodkin
- Evotec (UK) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
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10
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Abstract
The vast increase of recently solved GPCR X-ray structures forms the basis for GPCR homology modeling to atomistic accuracy. Nowadays, homology models can be employed for GPCR-ligand optimization and have been reported as invaluable tools for drug design in the last few years. Elucidation of the complex GPCR pharmacology and the associated GPCR conformations made clear that different homology models have to be constructed for different activation states of the GPCRs. Therefore, templates have to be chosen accordingly to their sequence homology as well as to their activation state. The subsequent ligand placement is nontrivial, as some recent X-ray structures show very unusual ligand binding sites and solvent involvement, expanding the space of the putative ligand binding site from the generic retinal binding pocket to the whole receptor. In the present study, a workflow is presented starting from the selection of the target sequence, guiding through the GPCR modeling process, and finishing with ligand placement and pose validation.
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Affiliation(s)
- Christofer S Tautermann
- Department for Medicinal Chemistry, Boehringer Ingelheim Pharma, GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany.
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11
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Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. Structure 2018; 26:7-19.e5. [DOI: 10.1016/j.str.2017.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/02/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
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12
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Thompson MD, Sakurai T, Rainero I, Maj MC, Kukkonen JP. Orexin Receptor Multimerization versus Functional Interactions: Neuropharmacological Implications for Opioid and Cannabinoid Signalling and Pharmacogenetics. Pharmaceuticals (Basel) 2017; 10:ph10040079. [PMID: 28991183 PMCID: PMC5748636 DOI: 10.3390/ph10040079] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022] Open
Abstract
Orexins/hypocretins are neuropeptides formed by proteolytic cleavage of a precursor peptide, which are produced by neurons found in the lateral hypothalamus. The G protein-coupled receptors (GPCRs) for these ligands, the OX₁ and OX₂ orexin receptors, are more widely expressed throughout the central nervous system. The orexin/hypocretin system has been implicated in many pathways, and its dysregulation is under investigation in a number of diseases. Disorders in which orexinergic mechanisms are being investigated include narcolepsy, idiopathic sleep disorders, cluster headache and migraine. Human narcolepsy has been associated with orexin deficiency; however, it has only rarely been attributed to mutations in the gene encoding the precursor peptide. While gene variations within the canine OX₂ gene hcrtr2 have been directly linked with narcolepsy, the majority of human orexin receptor variants are weakly associated with diseases (the idiopathic sleep disorders, cluster headache and polydipsia-hyponatremia in schizophrenia) or are of potential pharmacogenetic significance. Evidence for functional interactions and/or heterodimerization between wild-type and variant orexin receptors and opioid and cannabinoid receptors is discussed in the context of its relevance to depression and epilepsy.
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Affiliation(s)
- Miles D Thompson
- Department of Pediatrics, University of California, San Diego 92093, CA, USA.
| | - Takeshi Sakurai
- Department of Molecular Neuroscience and Integrative Physiology, Faculty of Medicine, Kanazawa University, Kanazawa 920-8620, Japan.
| | - Innocenzo Rainero
- Department of Neuroscience, University of Turin, Torino 10124, Italy.
| | - Mary C Maj
- Department of Biochemistry, School of Medicine, Saint George's University, Saint George's 11739, Grenada.
| | - Jyrki P Kukkonen
- Biochemistry and Cell Biology, Department of Veterinary Biosciences, University of Helsinki, Helsinki 11739, Finland.
- Department of Physiology, Institute of Biomedicine, Biomedicum Helsinki, University of Helsinki, Helsinki 00100, Finland.
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13
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Abstract
The human orexin/hypocretin receptors (hOX1R and hOX2R) are G protein-coupled receptors (GPCRs) that mediate the diverse functions of the orexin/hypocretin neuropeptides. Orexins/hypocretins produced by neurons in the lateral hypothalamus stimulate their cognate GPCRs in multiple regions of the central nervous system to control sleep and arousal, circadian rhythms, metabolism, reward pathways, and other behaviors. Dysfunction of orexin/hypocretin signaling is associated with human disease, and the receptors are active targets in a number of therapeutic areas. To better understand the molecular mechanism of the orexin/hypocretin neuropeptides, high-resolution three-dimensional structures of hOX1R and hOX2R are critical. We have solved high-resolution crystal structures of both human orexin/hypocretin receptors bound to high-affinity antagonists. These atomic structures have elucidated how different small molecule antagonists bind with high potency and selectivity, and have also provided clues as to how the native ligands may associate with their receptors. The orexin/hypocretin receptor coordinates, now available to the broader academic and drug discovery community, will facilitate rational design of new therapeutics that modulate orexin/hypocretin signaling in humans.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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14
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Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions. Biochem Soc Trans 2016; 44:574-81. [PMID: 27068972 PMCID: PMC5264495 DOI: 10.1042/bst20150250] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 12/11/2022]
Abstract
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.
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15
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Heifetz A, James T, Morao I, Bodkin MJ, Biggin PC. Guiding lead optimization with GPCR structure modeling and molecular dynamics. Curr Opin Pharmacol 2016; 30:14-21. [DOI: 10.1016/j.coph.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023]
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16
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Turku A, Borrel A, Leino TO, Karhu L, Kukkonen JP, Xhaard H. Pharmacophore Model To Discover OX1 and OX2 Orexin Receptor Ligands. J Med Chem 2016; 59:8263-75. [DOI: 10.1021/acs.jmedchem.6b00333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ainoleena Turku
- Faculty of Pharmacy,
Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66, FIN-00014 Helsinki, Finland
| | - Alexandre Borrel
- Faculty of Pharmacy,
Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland
| | - Teppo O. Leino
- Faculty of Pharmacy,
Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland
| | - Lasse Karhu
- Faculty of Pharmacy,
Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland
| | - Jyrki P. Kukkonen
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66, FIN-00014 Helsinki, Finland
| | - Henri Xhaard
- Faculty of Pharmacy,
Division of Pharmaceutical Chemistry and Technology, University of Helsinki, P.O. Box 56, FIN-00014 Helsinki, Finland
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17
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Heidmann B, Gatfield J, Roch C, Treiber A, Tortoioli S, Brotschi C, Williams JT, Bolli MH, Abele S, Sifferlen T, Jenck F, Boss C. Discovery of Highly Potent Dual Orexin Receptor Antagonists via a Scaffold-Hopping Approach. ChemMedChem 2016; 11:2132-2146. [DOI: 10.1002/cmdc.201600175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/18/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Bibia Heidmann
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - John Gatfield
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Catherine Roch
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Alexander Treiber
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Simone Tortoioli
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Christine Brotschi
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Jodi T. Williams
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Martin H. Bolli
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Stefan Abele
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Thierry Sifferlen
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - François Jenck
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
| | - Christoph Boss
- Actelion Pharmaceuticals Ltd.; Drug Discovery and Preclinical Research & Development; Gewerbestrasse 16 4123 Allschwil Switzerland
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18
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Heifetz A, Storer RI, McMurray G, James T, Morao I, Aldeghi M, Bodkin MJ, Biggin PC. Application of an Integrated GPCR SAR-Modeling Platform To Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B. ACS Chem Biol 2016; 11:1372-82. [PMID: 26900768 DOI: 10.1021/acschembio.5b01045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Agonism of the 5-HT2C serotonin receptor has been associated with the treatment of a number of diseases including obesity, psychiatric disorders, sexual health, and urology. However, the development of effective 5-HT2C agonists has been hampered by the difficulty in obtaining selectivity over the closely related 5-HT2B receptor, agonism of which is associated with irreversible cardiac valvulopathy. Understanding how to design selective agonists requires exploration of the structural features governing the functional uniqueness of the target receptor relative to related off targets. X-ray crystallography, the major experimental source of structural information, is a slow and challenging process for integral membrane proteins, and so is currently not feasible for every GPCR or GPCR-ligand complex. Therefore, the integration of existing ligand SAR data with GPCR modeling can be a practical alternative to provide this essential structural insight. To demonstrate this, we integrated SAR data from 39 azepine series 5-HT2C agonists, comprising both selective and unselective examples, with our hierarchical GPCR modeling protocol (HGMP). Through this work we have been able to demonstrate how relatively small differences in the amino acid sequences of GPCRs can lead to significant differences in secondary structure and function, as supported by experimental data. In particular, this study suggests that conformational differences in the tilt of TM7 between 5-HT2B and 5-HT2C, which result from differences in interhelical interactions, may be the major source of selectivity in G-protein activation between these two receptors. Our approach also demonstrates how the use of GPCR models in conjunction with SAR data can be used to explain activity cliffs.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | | | | | - Tim James
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Mike J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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19
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Yin J, Babaoglu K, Brautigam CA, Clark L, Shao Z, Scheuermann TH, Harrell CM, Gotter AL, Roecker AJ, Winrow CJ, Renger JJ, Coleman PJ, Rosenbaum DM. Structure and ligand-binding mechanism of the human OX1 and OX2 orexin receptors. Nat Struct Mol Biol 2016; 23:293-9. [PMID: 26950369 DOI: 10.1038/nsmb.3183] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/02/2016] [Indexed: 01/10/2023]
Abstract
The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) regulate sleep and other behavioral functions in mammals, and are therapeutic targets for sleep and wake disorders. The human receptors hOX1R and hOX2R, which are 64% identical in sequence, have overlapping but distinct physiological functions and potential therapeutic profiles. We determined structures of hOX1R bound to the OX1R-selective antagonist SB-674042 and the dual antagonist suvorexant at 2.8-Å and 2.75-Å resolution, respectively, and used molecular modeling to illuminate mechanisms of antagonist subtype selectivity between hOX1R and hOX2R. The hOX1R structures also reveal a conserved amphipathic α-helix, in the extracellular N-terminal region, that interacts with orexin-A and is essential for high-potency neuropeptide activation at both receptors. The orexin-receptor crystal structures are valuable tools for the design and development of selective orexin-receptor antagonists and agonists.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kerim Babaoglu
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Chad A Brautigam
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lindsay Clark
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zhenhua Shao
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas H Scheuermann
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Charles M Harrell
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Anthony L Gotter
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Anthony J Roecker
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Christopher J Winrow
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - John J Renger
- Department of Neuroscience, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Paul J Coleman
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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20
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Biggin PC, Aldeghi M, Bodkin MJ, Heifetz A. Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:161-181. [PMID: 27553242 DOI: 10.1007/978-3-319-35072-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.
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Affiliation(s)
- Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael J Bodkin
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Alexander Heifetz
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
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21
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GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014. Naunyn Schmiedebergs Arch Pharmacol 2015; 388:883-903. [PMID: 25772061 PMCID: PMC4495723 DOI: 10.1007/s00210-015-1111-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
Abstract
G-protein coupled receptors (GPCRs) are the targets of over half of all prescribed drugs today. The UniProt database has records for about 800 proteins classified as GPCRs, but drugs have only been developed against 50 of these. Thus, there is huge potential in terms of the number of targets for new therapies to be designed. Several breakthroughs in GPCRs biased pharmacology, structural biology, modelling and scoring have resulted in a resurgence of interest in GPCRs as drug targets. Therefore, an international conference, sponsored by the Royal Society, with world-renowned researchers from industry and academia was recently held to discuss recent progress and highlight key areas of future research needed to accelerate GPCR drug discovery. Several key points emerged. Firstly, structures for all three major classes of GPCRs have now been solved and there is increasing coverage across the GPCR phylogenetic tree. This is likely to be substantially enhanced with data from x-ray free electron sources as they move beyond proof of concept. Secondly, the concept of biased signalling or functional selectivity is likely to be prevalent in many GPCRs, and this presents exciting new opportunities for selectivity and the control of side effects, especially when combined with increasing data regarding allosteric modulation. Thirdly, there will almost certainly be some GPCRs that will remain difficult targets because they exhibit complex ligand dependencies and have many metastable states rendering them difficult to resolve by crystallographic methods. Subtle effects within the packing of the transmembrane helices are likely to mask and contribute to this aspect, which may play a role in species dependent behaviour. This is particularly important because it has ramifications for how we interpret pre-clinical data. In summary, collaborative efforts between industry and academia have delivered significant progress in terms of structure and understanding of GPCRs and will be essential for resolving problems associated with the more difficult targets in the future.
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22
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Neveu C, Dulin F, Lefranc B, Galas L, Calbrix C, Bureau R, Rault S, Chuquet J, Boutin JA, Guilhaudis L, Ségalas-Milazzo I, Vaudry D, Vaudry H, Santos JSDO, Leprince J. Molecular basis of agonist docking in a human GPR103 homology model by site-directed mutagenesis and structure-activity relationship studies. Br J Pharmacol 2014; 171:4425-39. [PMID: 24913445 DOI: 10.1111/bph.12808] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 04/04/2014] [Accepted: 05/15/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND AND PURPOSE The neuropeptide 26RFa and its cognate receptor GPR103 are involved in the control of food intake and bone mineralization. Here, we have tested, experimentally, the predicted ligand-receptor interactions by site-directed mutagenesis of GPR103 and designed point-substituted 26RFa analogues. EXPERIMENTAL APPROACH Using the X-ray structure of the β2 -adrenoceptor, a 3-D molecular model of GPR103 has been built. The bioactive C-terminal octapeptide 26RFa(19-26) , KGGFSFRF-NH2 , was docked in this GPR103 model and the ligand-receptor complex was submitted to energy minimization. KEY RESULTS In the most stable complex, the Phe-Arg-Phe-NH2 part was oriented inside the receptor cavity, whereas the N-terminal Lys residue remained outside. A strong intermolecular interaction was predicted between the Arg(25) residue of 26RFa and the Gln(125) residue located in the third transmembrane helix of GPR103. To confirm this interaction experimentally, we tested the ability of 26RFa and Arg-modified 26RFa analogues to activate the wild-type and the Q125A mutant receptors transiently expressed in CHO cells. 26RFa (10(-6) M) enhanced [Ca(2+) ]i in wild-type GPR103-transfected cells, but failed to increase [Ca(2+) ]i in Q125A mutant receptor-expressing cells. Moreover, asymmetric dimethylation of the side chain of arginine led to a 26RFa analogue, [ADMA(25) ]26RFa(20-26) , that was unable to activate the wild-type GPR103, but antagonized 26RFa-evoked [Ca(2+) ]i increase. CONCLUSION AND IMPLICATIONS Altogether, these data provide strong evidence for a functional interaction between the Arg(25) residue of 26RFa and the Gln(125) residue of GPR103 upon ligand-receptor activation, which can be exploited for the rational design of potent GPR103 agonists and antagonists.
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Affiliation(s)
- C Neveu
- Inserm U982, Laboratory of Neuronal and Neuroendocrine Cell Differentiation and Communication, Neurotrophic Factors and Neuronal Differentiation Team, Institute for Research and Innovation in Biomedicine (IRIB); Cell Imaging Platform of Normandy (PRIMACEN), IRIB; Normandie Univ, France
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23
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Abstract
Addiction is a chronic relapsing disorder which presents a significant global health burden and unmet medical need. The orexin/hypocretin system is an attractive potential therapeutic target as demonstrated by the successful clinical trials of antagonist medications like Suvorexant for insomnia. It is composed of two neuropeptides, orexin-A and orexin-B and two excitatory and promiscuous G-protein coupled receptors, OX1 and OX2. Orexins are known to have a variety of functions, most notably in regulating arousal, appetite and reward. The orexins have been shown to have a role in mediating the effects of several drugs of abuse, such as cocaine, morphine and alcohol via projections to key brain regions such as the ventral tegmental area, nucleus accumbens and prefrontal cortex. However, it has not yet been demonstrated whether the dual orexin receptor antagonists (DORAs) under development for insomnia are ideal drugs for the treatment of addiction. The question of whether to use a DORA or single orexin receptor antagonist (SORA) for the treatment of addiction is a key question that will need to be answered in order to maximize the clinical utility of orexin receptor antagonists. This review will examine the role of the orexin/hypocretin system in addiction, orexin-based pharmacotherapies under development and factors affecting the selection of one or both orexin receptors as drug targets for the treatment of addiction.
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24
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Leonis G, Avramopoulos A, Salmas RE, Durdagi S, Yurtsever M, Papadopoulos MG. Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. J Chem Inf Model 2014; 54:2294-308. [DOI: 10.1021/ci5002873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Georgios Leonis
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Aggelos Avramopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Ramin Ekhteiari Salmas
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Serdar Durdagi
- Department
of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Istanbul 34349, Turkey
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Manthos G. Papadopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
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25
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Thompson MD, Xhaard H, Sakurai T, Rainero I, Kukkonen JP. OX1 and OX2 orexin/hypocretin receptor pharmacogenetics. Front Neurosci 2014; 8:57. [PMID: 24834023 PMCID: PMC4018553 DOI: 10.3389/fnins.2014.00057] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 03/12/2014] [Indexed: 01/01/2023] Open
Abstract
Orexin/hypocretin peptide mutations are rare in humans. Even though human narcolepsy is associated with orexin deficiency, this is only extremely rarely due to mutations in the gene coding prepro-orexin, the precursor for both orexin peptides. In contrast, coding and non-coding variants of the OX1 and OX2 orexin receptors have been identified in many human populations; sometimes, these have been associated with disease phenotype, although most confer a relatively low risk. In most cases, these studies have been based on a candidate gene hypothesis that predicts the involvement of orexins in the relevant pathophysiological processes. In the current review, the known human OX1/HCRTR1 and OX2/HCRTR2 genetic variants/polymorphisms as well as studies concerning their involvement in disorders such as narcolepsy, excessive daytime sleepiness, cluster headache, polydipsia-hyponatremia in schizophrenia, and affective disorders are discussed. In most cases, the functional cellular or pharmacological correlates of orexin variants have not been investigated—with the exception of the possible impact of an amino acid 10 Pro/Ser variant of OX2 on orexin potency—leaving conclusions on the nature of the receptor variant effects speculative. Nevertheless, we present perspectives that could shape the basis for further studies. The pharmacology and other properties of the orexin receptor variants are discussed in the context of GPCR signaling. Since orexinergic therapeutics are emerging, the impact of receptor variants on the affinity or potency of ligands deserves consideration. This perspective (pharmacogenetics) is also discussed in the review.
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Affiliation(s)
- Miles D Thompson
- University of Toronto Epilepsy Research Program, Department of Pharmacology, University of Toronto Toronto, ON, Canada
| | - Henri Xhaard
- Faculty of Pharmacy, Centre for Drug Research, University of Helsinki Helsinki, Finland
| | - Takeshi Sakurai
- Department of Molecular Neuroscience and Integrative Physiology, Faculty of Medicine, Kanazawa University Kanazawa, Japan
| | | | - Jyrki P Kukkonen
- Biochemistry and Cell Biology, Department of Veterinary Biosciences, University of Helsinki Helsinki, Finland
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26
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Heifetz A, Barker O, Morris GB, Law R, Slack M, Biggin PC. Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis. Biochemistry 2013; 52:8246-60. [PMID: 24144388 PMCID: PMC3880013 DOI: 10.1021/bi401119m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/21/2013] [Indexed: 02/06/2023]
Abstract
The class A G-protein-coupled receptors (GPCRs) Orexin-1 (OX1) and Orexin-2 (OX2) are located predominantly in the brain and are linked to a range of different physiological functions, including the control of feeding, energy metabolism, modulation of neuro-endocrine function, and regulation of the sleep-wake cycle. The natural agonists for OX1 and OX2 are two neuropeptides, Orexin-A and Orexin-B, which have activity at both receptors. Site-directed mutagenesis (SDM) has been reported on both the receptors and the peptides and has provided important insight into key features responsible for agonist activity. However, the structural interpretation of how these data are linked together is still lacking. In this work, we produced and used SDM data, homology modeling followed by MD simulation, and ensemble-flexible docking to generate binding poses of the Orexin peptides in the OX receptors to rationalize the SDM data. We also developed a protein pairwise similarity comparing method (ProS) and a GPCR-likeness assessment score (GLAS) to explore the structural data generated within a molecular dynamics simulation and to help distinguish between different GPCR substates. The results demonstrate how these newly developed methods of structural assessment for GPCRs can be used to provide a working model of neuropeptide-Orexin receptor interaction.
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Affiliation(s)
- Alexander Heifetz
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - Oliver Barker
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - G. Benjamin Morris
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Richard
J. Law
- Evotec
(U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K.
| | - Mark Slack
- Evotec
AG, Manfred Eigen Campus,
Essener Bogen 7, 22419 Hamburg, Germany
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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27
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Xu B, Fällmar H, Boukharta L, Pruner J, Lundell I, Mohell N, Gutiérrez-de-Terán H, Aqvist J, Larhammar D. Mutagenesis and computational modeling of human G-protein-coupled receptor Y2 for neuropeptide Y and peptide YY. Biochemistry 2013; 52:7987-98. [PMID: 24111902 DOI: 10.1021/bi400830c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Neuropeptide Y and peptide YY receptor type 2 (Y2) is involved in appetite regulation and several other physiological processes. We have investigated the structure of the human Y2 receptor. Computational modeling of receptor-agonist interactions was used as a guide to design a series of receptor mutants, followed by binding assays using full-length and truncated peptide agonists and the Y2-specific antagonist BIIE0246. Our model suggested a hydrogen bond network among highly conserved residues Thr2.61, Gln3.32, and His7.39, which could play roles in ligand binding and/or receptor structure. In addition, the C-terminus of the peptide could make contact with residues Tyr5.38 and Leu6.51. Mutagenesis of all these positions, followed by binding assays, provides experimental support for our computational model: most of the mutants for the residues forming the proposed hydrogen bond network displayed reduced peptide agonist affinities as well as reduced hPYY3-36 potency in a functional assay. The Ala and Leu mutants of Gln3.32 and His7.39 disrupted membrane expression of the receptor. Combined with the modeling, the experimental results support roles for these hydrogen bond network residues in peptide binding as well as receptor architecture. The reduced agonist affinity for mutants of Tyr5.38 and Leu6.51 supports their role in a binding pocket surrounding the invariant tyrosine at position 36 of the peptide ligands. The results for antagonist BIIE0246 suggest several differences in interactions compared to those of the peptides. Our results lead to a new structural model for NPY family receptors and peptide binding.
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Affiliation(s)
- Bo Xu
- Department of Neuroscience, Science for Life Laboratory, Uppsala University , Box 593, SE-751 24 Uppsala, Sweden
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28
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Lebold TP, Bonaventure P, Shireman BT. Selective orexin receptor antagonists. Bioorg Med Chem Lett 2013; 23:4761-9. [PMID: 23891187 DOI: 10.1016/j.bmcl.2013.06.057] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/18/2013] [Accepted: 06/20/2013] [Indexed: 01/03/2023]
Abstract
The orexin, or hypocretin, neuropeptides (orexin-A and orexin-B) are produced on neurons in the hypothalamus which project to key areas of the brain that control sleep-wake states, modulation of food intake, panic, anxiety, emotion, reward and addictive behaviors. These neuropeptides exert their effects on a pair of G-protein coupled receptors termed the orexin-1 (OX1) and orexin-2 (OX2) receptors. Emerging biology suggests the involvement of these receptors in psychiatric disorders as they are thought to play a key role in the regulation of multiple systems. This review is intended to highlight key selective OX1 or OX2 small-molecule antagonists.
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Affiliation(s)
- Terry P Lebold
- Janssen Research & Development, 3210 Merryfield Row, San Diego, CA 92121, USA
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29
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Heifetz A, Barker O, Verquin G, Wimmer N, Meutermans W, Pal S, Law RJ, Whittaker M. Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites. J Chem Inf Model 2013; 53:1084-99. [PMID: 23590178 DOI: 10.1021/ci4000882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Obesity is an increasingly common disease. While antagonism of the melanin-concentrating hormone-1 receptor (MCH-1R) has been widely reported as a promising therapeutic avenue for obesity treatment, no MCH-1R antagonists have reached the market. Discovery and optimization of new chemical matter targeting MCH-1R is hindered by reduced HTS success rates and a lack of structural information about the MCH-1R binding site. X-ray crystallography and NMR, the major experimental sources of structural information, are very slow processes for membrane proteins and are not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of these methods to impact the drug discovery process for GPCR targets in "real-time", and hence, there is an urgent need for other practical and cost-efficient alternatives. We present here a conceptually pioneering approach that integrates GPCR modeling with design, synthesis, and screening of a diverse library of sugar-based compounds from the VAST technology (versatile assembly on stable templates) to provide structural insights on the MCH-1R binding site. This approach creates a cost-efficient new avenue for structure-based drug discovery (SBDD) against GPCR targets. In our work, a primary VAST hit was used to construct a high-quality MCH-1R model. Following model validation, a structure-based virtual screen yielded a 14% hit rate and 10 novel chemotypes of potent MCH-1R antagonists, including EOAI3367472 (IC50 = 131 nM) and EOAI3367474 (IC50 = 213 nM).
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK), Ltd., Milton Park, Abingdon, Oxfordshire, United Kingdom.
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30
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Characterization of the dynamic events of GPCRs by automated computational simulations. Biochem Soc Trans 2013; 41:205-12. [DOI: 10.1042/bst20120287] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The recent advances in membrane protein crystallography have provided extremely valuable structural information of the superfamily of GPCRs (G-protein-coupled receptors). This has been particularly true for a few receptors whose structure was solved several times under different biochemical conditions. It follows that the mechanisms of receptor conformational equilibrium and related dynamic events can be explored by computational simulations. In the present article, we summarize our recent understanding of several dynamic features of GPCRs, accomplished through the use of MD (molecular dynamics) simulations. Our pipeline for the MD simulations of GPCRs, implemented in the web service http://gpcr.usc.es, is updated in the present paper and illustrated by recent applications. Special emphasis is put on the A2A adenosine receptor, one of the selected cases where crystal structures in several conformations and conditions exist, and on the dimerization process of the CXCR4 (CXC chemokine receptor 4).
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31
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Schultes S, Nijmeijer S, Engelhardt H, Kooistra AJ, Vischer HF, de Esch IJP, Haaksma EEJ, Leurs R, de Graaf C. Mapping histamine H4 receptor–ligand binding modes. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20212c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Computational prediction of ligand binding modes in G protein-coupled receptors (GPCRs) remains a challenging task. Systematic consideration of different protein modelling templates, ligand binding poses, and ligand protonation states in extensive molecular dynamics (MD) simulation studies enabled the prediction of ligand-specific mutation effects in the histamine H4 receptor, a key player in inflammation.
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Affiliation(s)
- Sabine Schultes
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Saskia Nijmeijer
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Harald Engelhardt
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Albert J. Kooistra
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Henry F. Vischer
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Eric E. J. Haaksma
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Rob Leurs
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Chris de Graaf
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
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Kukkonen JP. Physiology of the orexinergic/hypocretinergic system: a revisit in 2012. Am J Physiol Cell Physiol 2012; 304:C2-32. [PMID: 23034387 DOI: 10.1152/ajpcell.00227.2012] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The neuropeptides orexins and their G protein-coupled receptors, OX(1) and OX(2), were discovered in 1998, and since then, their role has been investigated in many functions mediated by the central nervous system, including sleep and wakefulness, appetite/metabolism, stress response, reward/addiction, and analgesia. Orexins also have peripheral actions of less clear physiological significance still. Cellular responses to the orexin receptor activity are highly diverse. The receptors couple to at least three families of heterotrimeric G proteins and other proteins that ultimately regulate entities such as phospholipases and kinases, which impact on neuronal excitation, synaptic plasticity, and cell death. This article is a 10-year update of my previous review on the physiology of the orexinergic/hypocretinergic system. I seek to provide a comprehensive update of orexin physiology that spans from the molecular players in orexin receptor signaling to the systemic responses yet emphasizing the cellular physiological aspects of this system.
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Affiliation(s)
- Jyrki P Kukkonen
- Dept. of Veterinary Biosciences, University of Helsinki, Finland.
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