1
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Morales-Salazar I, Garduño-Albino CE, Montes-Enríquez FP, Nava-Tapia DA, Navarro-Tito N, Herrera-Zúñiga LD, González-Zamora E, Islas-Jácome A. Synthesis of Pyrrolo[3,4- b]pyridin-5-ones via Ugi-Zhu Reaction and In Vitro-In Silico Studies against Breast Carcinoma. Pharmaceuticals (Basel) 2023; 16:1562. [PMID: 38004428 PMCID: PMC10674953 DOI: 10.3390/ph16111562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
An Ugi-Zhu three-component reaction (UZ-3CR) coupled in a one-pot manner to a cascade process (N-acylation/aza Diels-Alder cycloaddition/decarboxylation/dehydration) was performed to synthesize a series of pyrrolo[3,4-b]pyridin-5-ones in 20% to 92% overall yields using ytterbium triflate as a catalyst, toluene as a solvent, and microwaves as a heat source. The synthesized molecules were evaluated in vitro against breast cancer cell lines MDA-MB-231 and MCF-7, finding that compound 1f, at a concentration of 6.25 μM, exhibited a potential cytotoxic effect. Then, to understand the interactions between synthesized compounds and the main proteins related to the cancer cell lines, docking studies were performed on the serine/threonine kinase 1 (AKT1) and Orexetine type 2 receptor (Ox2R), finding moderate to strong binding energies, which matched accurately with the in vitro results. Additionally, molecular dynamics were performed between proteins related to the studied cell lines and the three best ligands.
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Affiliation(s)
- Ivette Morales-Salazar
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
| | - Carlos E. Garduño-Albino
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
| | - Flora P. Montes-Enríquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
| | - Dania A. Nava-Tapia
- Laboratorio de Biología Celular del Cáncer, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
| | - Napoleón Navarro-Tito
- Laboratorio de Biología Celular del Cáncer, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, Mexico;
| | - Leonardo David Herrera-Zúñiga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
| | - Eduardo González-Zamora
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
| | - Alejandro Islas-Jácome
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, Ciudad de México 09340, Mexico; (I.M.-S.); (C.E.G.-A.); (F.P.M.-E.); (E.G.-Z.)
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2
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Ippolito M, De Pascali F, Hopfinger N, Komolov KE, Laurinavichyute D, Reddy PAN, Sakkal LA, Rajkowski KZ, Nayak AP, Lee J, Lee J, Cao G, Donover PS, Reichman M, An SS, Salvino JM, Penn RB, Armen RS, Scott CP, Benovic JL. Identification of a β-arrestin-biased negative allosteric modulator for the β 2-adrenergic receptor. Proc Natl Acad Sci U S A 2023; 120:e2302668120. [PMID: 37490535 PMCID: PMC10401000 DOI: 10.1073/pnas.2302668120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/26/2023] [Indexed: 07/27/2023] Open
Abstract
Catecholamine-stimulated β2-adrenergic receptor (β2AR) signaling via the canonical Gs-adenylyl cyclase-cAMP-PKA pathway regulates numerous physiological functions, including the therapeutic effects of exogenous β-agonists in the treatment of airway disease. β2AR signaling is tightly regulated by GRKs and β-arrestins, which together promote β2AR desensitization and internalization as well as downstream signaling, often antithetical to the canonical pathway. Thus, the ability to bias β2AR signaling toward the Gs pathway while avoiding β-arrestin-mediated effects may provide a strategy to improve the functional consequences of β2AR activation. Since attempts to develop Gs-biased agonists and allosteric modulators for the β2AR have been largely unsuccessful, here we screened small molecule libraries for allosteric modulators that selectively inhibit β-arrestin recruitment to the receptor. This screen identified several compounds that met this profile, and, of these, a difluorophenyl quinazoline (DFPQ) derivative was found to be a selective negative allosteric modulator of β-arrestin recruitment to the β2AR while having no effect on β2AR coupling to Gs. DFPQ effectively inhibits agonist-promoted phosphorylation and internalization of the β2AR and protects against the functional desensitization of β-agonist mediated regulation in cell and tissue models. The effects of DFPQ were also specific to the β2AR with minimal effects on the β1AR. Modeling, mutagenesis, and medicinal chemistry studies support DFPQ derivatives binding to an intracellular membrane-facing region of the β2AR, including residues within transmembrane domains 3 and 4 and intracellular loop 2. DFPQ thus represents a class of biased allosteric modulators that targets an allosteric site of the β2AR.
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Affiliation(s)
- Michael Ippolito
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Francesco De Pascali
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Nathan Hopfinger
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Konstantin E. Komolov
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Daniela Laurinavichyute
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | | | - Leon A. Sakkal
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, PA19107
| | - Kyle Z. Rajkowski
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, PA19107
| | - Ajay P. Nayak
- Center for Translational Medicine, Department of Medicine, and Jane and Leonard Korman Respiratory Institute, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Justin Lee
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ08901
| | - Jordan Lee
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ08901
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ08901
| | | | | | - Steven S. An
- Rutgers Institute for Translational Medicine and Science, New Brunswick, NJ08901
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ08854
| | | | - Raymond B. Penn
- Center for Translational Medicine, Department of Medicine, and Jane and Leonard Korman Respiratory Institute, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Roger S. Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, PA19107
| | - Charles P. Scott
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Jeffrey L. Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
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3
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Ball HL, Said H, Chapman K, Fu R, Xiong Y, Burk JA, Rosenbaum D, Veneziano R, Cotten ML. Orexin A, an amphipathic α-helical neuropeptide involved in pleiotropic functions in the nervous and immune systems: Synthetic approach and biophysical studies of the membrane-bound state. Biophys Chem 2023; 297:107007. [PMID: 37037119 DOI: 10.1016/j.bpc.2023.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
This research reports on the membrane interactions of orexin A (OXA), an α-helical and amphipathic neuropeptide that contains 33 residues and two disulfide bonds in the N-terminal region. OXA, which activates the orexins 1 and 2 receptors in neural and immune cell membranes, has essential pleiotropic physiological effects, including at the levels of arousal, sleep/wakefulness, energy balance, neuroprotection, lipid signaling, the inflammatory response, and pain. As a result, the orexin system has become a prominent target to treat diseases such as sleep disorders, drug addiction, and inflammation. While the high-resolution structure of OXA has been investigated in water and bound to micelles, there is a lack of information about its conformation bound to phospholipid membranes and its receptors. NMR is a powerful method to investigate peptide structures in a membrane environment. To facilitate the NMR structural studies of OXA exposed to membranes, we present a novel synthetic scheme, leading to the production of isotopically-labeled material at high purity. A receptor activation assay shows that the 15N-labeled peptide is biologically active. Biophysical studies are performed using surface plasmon resonance, circular dichroism, and NMR to investigate the interactions of OXA with phospholipid bilayers. The results demonstrate a strong interaction between the peptide and phospholipids, an increase in α-helical content upon membrane binding, and an in-plane orientation of the C-terminal region critical to function. This new knowledge about structure-activity relationships in OXA could inspire the design of novel therapeutics that leverage the anti-inflammatory and neuro-protective functions of OXA, and therefore could help address neuroinflammation, a major issue associated with neurological disorders such as Alzheimer's disease.
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Affiliation(s)
- Haydn L Ball
- Department of Chemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hooda Said
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Karen Chapman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yawei Xiong
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA
| | - Joshua A Burk
- Department of Psychological Sciences, William & Mary, Williamsburg, VA 23185, USA
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Remi Veneziano
- Department of Bioengineering, College of Engineering and Computing, George Mason University, Fairfax, VA 22030, USA
| | - Myriam L Cotten
- Department of Applied Science, William & Mary, Williamsburg, VA 23185, USA.
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4
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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5
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Farrokhpour H, Bamdad F, Ashrafizaadeh M. Interaction between the Human OX2 Orexin Receptor and Suvorexant and Some of Its Analogues: SAPT (DFT) Interaction Energy Decomposition Analysis. J Phys Chem B 2022; 126:7528-7540. [PMID: 36166366 DOI: 10.1021/acs.jpcb.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the interaction energy (Eint) of suvorexant (as an orexin receptor antagonist) and some of its analogues with the important residues of the human OX2 orexin receptor, determined by molecular docking, is calculated using the symmetry-adapted perturbation theory-density functional theory (SAPT (DFT)) method. Also, the important residues with the dominant interaction with each ligand are determined based on the obtained SAPT (DFT) interaction energies. To analyze the interaction of the receptor with each ligand, the decomposition of Eint to its constituent components including electrostatic (Eele), exchange (Eex), induction (Eind), and exchange-induction (Eex-ind), dispersion (Edisp), and exchange-dispersion (Eex-disp) is performed. The change of interaction energy components with the replacement of the benzoxazole part of suvorexant by pyrimidine containing different functional groups, thieno pyrimidine, and furo pyrimidine is also investigated, separately. It is found that the change in Eint, due to these replacements, is controlled more by the variation of the electrostatic interaction energy component of Eint than by the other interaction energy components. A linear correlation (R2 = 0.91) is found for the variation of Eint versus experimental ligand-binding affinities. Also, the existence of the linear correlation for the variation of the interaction energy components with experimental ligand-binding affinities is investigated. The variation of the electrostatic component versus experimental ligand-binding affinities shows a more linear correlation compared to the other interaction energy components.
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Affiliation(s)
- Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Fatemeh Bamdad
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Mahmud Ashrafizaadeh
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
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6
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Abstract
The hypocretins (Hcrts), also known as orexins, are two neuropeptides produced exclusively in the lateral hypothalamus. They act on two specific receptors that are widely distributed across the brain and involved in a myriad of neurophysiological functions that include sleep, arousal, feeding, reward, fear, anxiety and cognition. Hcrt cell loss in humans leads to narcolepsy with cataplexy (narcolepsy type 1), a disorder characterized by intrusions of sleep into wakefulness, demonstrating that the Hcrt system is nonredundant and essential for sleep/wake stability. The causal link between Hcrts and arousal/wakefulness stabilisation has led to the development of a new class of drugs, Hcrt receptor antagonists to treat insomnia, based on the assumption that blocking orexin-induced arousal will facilitate sleep. This has been clinically validated: currently, two Hcrt receptor antagonists are approved to treat insomnia (suvorexant and lemborexant), with a New Drug Application recently submitted to the US Food and Drug Administration for a third drug (daridorexant). Other therapeutic applications under investigation include reduction of cravings in substance-use disorders and prevention of neurodegenerative disorders such as Alzheimer's disease, given the apparent bidirectional relationship between poor sleep and worsening of the disease. Circuit neuroscience findings suggest that the Hcrt system is a hub that integrates diverse inputs modulating arousal (e.g., circadian rhythms, metabolic status, positive and negative emotions) and conveys this information to multiple output regions. This neuronal architecture explains the wealth of physiological functions associated with Hcrts and highlights the potential of the Hcrt system as a therapeutic target for a number of disorders. We discuss present and future possible applications of drugs targeting the Hcrt system for the treatment of circuit-related neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Laura H Jacobson
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Dementia Research Centre, The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel Hoyer
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
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7
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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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8
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Yokoi S, Mitsutake A. Characteristic structural difference between inactive and active states of orexin 2 receptor determined using molecular dynamics simulations. Biophys Rev 2021; 14:221-231. [DOI: 10.1007/s12551-021-00862-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
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9
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Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation. Nat Commun 2021; 12:815. [PMID: 33547286 PMCID: PMC7864924 DOI: 10.1038/s41467-021-21087-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Narcolepsy type 1 (NT1) is a chronic neurological disorder that impairs the brain’s ability to control sleep-wake cycles. Current therapies are limited to the management of symptoms with modest effectiveness and substantial adverse effects. Agonists of the orexin receptor 2 (OX2R) have shown promise as novel therapeutics that directly target the pathophysiology of the disease. However, identification of drug-like OX2R agonists has proven difficult. Here we report cryo-electron microscopy structures of active-state OX2R bound to an endogenous peptide agonist and a small-molecule agonist. The extended carboxy-terminal segment of the peptide reaches into the core of OX2R to stabilize an active conformation, while the small-molecule agonist binds deep inside the orthosteric pocket, making similar key interactions. Comparison with antagonist-bound OX2R suggests a molecular mechanism that rationalizes both receptor activation and inhibition. Our results enable structure-based discovery of therapeutic orexin agonists for the treatment of NT1 and other hypersomnia disorders. Agonists of the orexin receptor 2 (OX2R) show promise in the treatment of narcolepsy. Cryo-EM structures of active-state OX2R bound to an endogenous peptide agonist and a small-molecule agonist suggest a molecular mechanism that rationalizes both receptor activation and inhibition.
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10
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Abstract
Twenty-two years after their discovery, the hypocretins (Hcrts), also known as orexins, are two of the most studied peptidergic systems, involved in myriad physiological systems that range from sleep, arousal, motivation, homeostatic regulation, fear, anxiety and learning. A causal relationship between activity of Hcrt and arousal stability was established shortly after their discovery and have led to the development of a new class of drugs to treat insomnia. In this review we discuss the many faces of the Hcrt system and examine recent findings that implicate decreased Hcrt function in the pathogenesis of a number of neuropsychiatric conditions. We also discuss future therapeutic strategies to replace or enhance Hcrt function as a treatment option for these neuropsychiatric conditions.
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Affiliation(s)
- Erica Seigneur
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA
| | - Luis de Lecea
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA
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11
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Tikhonova IG, Gigoux V, Fourmy D. Understanding Peptide Binding in Class A G Protein-Coupled Receptors. Mol Pharmacol 2019; 96:550-561. [PMID: 31436539 DOI: 10.1124/mol.119.115915] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Many physiologic processes are controlled through the activation of G protein-coupled receptors (GPCRs) by regulatory peptides, making peptide GPCRs particularly useful targets for major human diseases such as diabetes and cancer. Peptide GPCRs are also being evaluated as next-generation targets for the development of novel antiparasite agents and insecticides in veterinary medicine and agriculture. Resolution of crystal structures for several peptide GPCRs has advanced our understanding of peptide-receptor interactions and fueled interest in correlating peptide heterogeneity with receptor-binding properties. In this review, the knowledge of recently crystalized peptide-GPCR complexes, previously accumulated peptide structure-activity relationship studies, receptor mutagenesis, and sequence alignment are integrated to better understand peptide binding to the transmembrane cavity of class A GPCRs. Using SAR data, we show that peptide class A GPCRs can be divided into groups with distinct hydrophilic residues. These characteristic residues help explain the preference of a receptor to bind the C-terminal free carboxyl group, the C-terminal amidated group, or the N-terminal ammonium group of peptides.
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Affiliation(s)
- Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom, (I.G.T.) and INSERM ERL1226-Receptology and Therapeutic Targeting of Cancers, Laboratoire de Physique et Chimie des Nano-Objets, CNRS UMR5215-INSA, Université de Toulouse III, Toulouse, France (V.G., D.F.)
| | - Veronique Gigoux
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom, (I.G.T.) and INSERM ERL1226-Receptology and Therapeutic Targeting of Cancers, Laboratoire de Physique et Chimie des Nano-Objets, CNRS UMR5215-INSA, Université de Toulouse III, Toulouse, France (V.G., D.F.)
| | - Daniel Fourmy
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom, (I.G.T.) and INSERM ERL1226-Receptology and Therapeutic Targeting of Cancers, Laboratoire de Physique et Chimie des Nano-Objets, CNRS UMR5215-INSA, Université de Toulouse III, Toulouse, France (V.G., D.F.)
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12
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Karhu L, Magarkar A, Bunker A, Xhaard H. Determinants of Orexin Receptor Binding and Activation-A Molecular Dynamics Study. J Phys Chem B 2019; 123:2609-2622. [PMID: 30786708 PMCID: PMC6727383 DOI: 10.1021/acs.jpcb.8b10220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
We
assess the stability of two previously suggested binding modes
for the neuropeptide orexin-A in the OX2 receptor through
extensive molecular dynamics simulations. As the activation determinants
of the receptor remain unknown, we simulated an unliganded receptor
and two small-molecular ligands, the antagonist suvorexant and the
agonist Nag26 for comparison. Each system was simulated in pure POPC
membrane as well as in the 25% cholesterol–POPC membrane. In
total, we carried out 36 μs of simulations. Through this set
of simulations, we report a stable binding mode for the C-terminus
of orexin-A. In addition, we suggest interactions that would promote
orexin receptor activation, as well as others that would stabilize
the inactive state.
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Affiliation(s)
- Lasse Karhu
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy , University of Helsinki , POB 56, FI-00014 Helsinki , Finland
| | - Aniket Magarkar
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , POB 56 , FI-00014 Helsinki , Finland
| | - Alex Bunker
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy , University of Helsinki , POB 56 , FI-00014 Helsinki , Finland
| | - Henri Xhaard
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy , University of Helsinki , POB 56, FI-00014 Helsinki , Finland
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Janockova J, Dolezal R, Nepovimova E, Kobrlova T, Benkova M, Kuca K, Konecny J, Mezeiova E, Melikova M, Hepnarova V, Ring A, Soukup O, Korabecny J. Investigation of New Orexin 2 Receptor Modulators Using In Silico and In Vitro Methods. Molecules 2018; 23:molecules23112926. [PMID: 30423961 PMCID: PMC6278354 DOI: 10.3390/molecules23112926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/02/2018] [Accepted: 11/08/2018] [Indexed: 11/16/2022] Open
Abstract
The neuropeptides, orexin A and orexin B (also known as hypocretins), are produced in hypothalamic neurons and belong to ligands for orphan G protein-coupled receptors. Generally, the primary role of orexins is to act as excitatory neurotransmitters and regulate the sleep process. Lack of orexins may lead to sleep disorder narcolepsy in mice, dogs, and humans. Narcolepsy is a neurological disorder of alertness characterized by a decrease of ability to manage sleep-wake cycles, excessive daytime sleepiness, and other symptoms, such as cataplexy, vivid hallucinations, and paralysis. Thus, the discovery of orexin receptors, modulators, and their causal implication in narcolepsy is the most important advance in sleep-research. The presented work is focused on the evaluation of compounds L1–L11 selected by structure-based virtual screening for their ability to modulate orexin receptor type 2 (OX2R) in comparison with standard agonist orexin-A together with their blood-brain barrier permeability and cytotoxicity. We can conclude that the studied compounds possess an affinity towards the OX2R. However, the compounds do not have intrinsic activity and act as the antagonists of this receptor. It was shown that L4 was the most potent antagonistic ligand to orexin A and displayed an IC50 of 2.2 µM, offering some promise mainly for the treatment of insomnia.
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Affiliation(s)
- Jana Janockova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Rafael Dolezal
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
- Center for Basic and Applied Research, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Tereza Kobrlova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic.
| | - Marketa Benkova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
| | - Kamil Kuca
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Jan Konecny
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Eva Mezeiova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
| | - Michaela Melikova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic.
| | - Vendula Hepnarova
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic.
| | - Avi Ring
- Norwegian Defence Research Establishment, Gunnar Randersvei 42, 2007 Kjeller, Norway.
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic.
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 05 Hradec Kralove, Czech Republic.
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14
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Karhu L, Weisell J, Turunen PM, Leino TO, Pätsi H, Xhaard H, Kukkonen JP, Wallén EAA. Stapled truncated orexin peptides as orexin receptor agonists. Peptides 2018; 102:54-60. [PMID: 29475074 DOI: 10.1016/j.peptides.2018.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/29/2018] [Accepted: 02/16/2018] [Indexed: 10/18/2022]
Abstract
The peptides orexin-A and -B, the endogenous agonists of the orexin receptors, have similar 19-amino-acid C-termini which retain full maximum response as truncated peptides with only marginally reduced potency, while further N-terminal truncations successively reduce the activity. The peptides have been suggested to bind in an α-helical conformation, and truncation beyond a certain critical length is likely to disrupt the overall helical structure. In this study, we set out to stabilize the α-helical conformation of orexin-A15-33 via peptide stapling at four different sites. At a suggested hinge region, we varied the length of the cross-linker as well as replaced the staple with two α-aminoisobutyric acid residues. Modifications close to the peptide C-terminus, which is crucial for activity, were not allowed. However, central and N-terminal modifications yielded bioactive peptides, albeit with decreased potencies. This provides evidence that the orexin receptors can accommodate and be activated by α-helical peptides. The decrease in potency is likely linked to a stabilization of suboptimal peptide conformation or blocking of peptide backbone-receptor interactions at the hinge region by the helical stabilization or the modified amino acids.
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Affiliation(s)
- Lasse Karhu
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, POB 56, FI-00014 University of Helsinki, Finland.
| | - Janne Weisell
- School of Pharmacy, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland.
| | - Pauli M Turunen
- Biochemistry and Cell Biology, Department of Veterinary Biosciences, Faculty of Veterinary Medicine, POB 66, FI-00014, University of Helsinki, Finland; Department of Physiology, Institute of Biomedicine, Biomedicum Helsinki, POB 63, FI-00014 University of Helsinki, Finland.
| | - Teppo O Leino
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, POB 56, FI-00014 University of Helsinki, Finland.
| | - Henri Pätsi
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, POB 56, FI-00014 University of Helsinki, Finland.
| | - Henri Xhaard
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, POB 56, FI-00014 University of Helsinki, Finland.
| | - Jyrki P Kukkonen
- Biochemistry and Cell Biology, Department of Veterinary Biosciences, Faculty of Veterinary Medicine, POB 66, FI-00014, University of Helsinki, Finland; Department of Physiology, Institute of Biomedicine, Biomedicum Helsinki, POB 63, FI-00014 University of Helsinki, Finland.
| | - Erik A A Wallén
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, POB 56, FI-00014 University of Helsinki, Finland.
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15
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In-silico guided discovery of novel CCR9 antagonists. J Comput Aided Mol Des 2018; 32:573-582. [DOI: 10.1007/s10822-018-0113-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
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16
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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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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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18
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Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Sci Rep 2017; 7:8223. [PMID: 28811548 PMCID: PMC5557796 DOI: 10.1038/s41598-017-08344-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022] Open
Abstract
Bitter taste is one of the basic taste modalities, warning against consuming potential poisons. Bitter compounds activate members of the bitter taste receptor (Tas2r) subfamily of G protein-coupled receptors (GPCRs). The number of functional Tas2rs is species-dependent. Chickens represent an intriguing minimalistic model, because they detect the bitter taste of structurally different molecules with merely three bitter taste receptor subtypes. We investigated the binding modes of several known agonists of a representative chicken bitter taste receptor, ggTas2r1. Because of low sequence similarity between ggTas2r1 and crystallized GPCRs (~10% identity, ~30% similarity at most), the combination of computational approaches with site-directed mutagenesis was used to characterize the agonist-bound conformation of ggTas2r1 binding site between TMs 3, 5, 6 and 7. We found that the ligand interactions with N93 in TM3 and/or N247 in TM5, combined with hydrophobic contacts, are typically involved in agonist recognition. Next, the ggTas2r1 structural model was successfully used to identify three quinine analogues (epiquinidine, ethylhydrocupreine, quinidine) as new ggTas2r1 agonists. The integrated approach validated here may be applicable to additional cases where the sequence identity of the GPCR of interest and the existing experimental structures is low.
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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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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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21
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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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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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23
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Nicole P, Couvineau P, Jamin N, Voisin T, Couvineau A. Crucial role of the orexin-B C-terminus in the induction of OX1 receptor-mediated apoptosis: analysis by alanine scanning, molecular modelling and site-directed mutagenesis. Br J Pharmacol 2015; 172:5211-23. [PMID: 26282891 PMCID: PMC4687804 DOI: 10.1111/bph.13287] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/12/2015] [Accepted: 08/11/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND PURPOSE Orexins (A and B) are hypothalamic peptides that interact with OX1 and OX2 receptors and are involved in the sleep/wake cycle. We previously demonstrated that OX1 receptors are highly expressed in colon cancer tumours and colonic cancer cell lines where orexins induce apoptosis and inhibit tumour growth in preclinical animal models. The present study explored the structure-function relationships of orexin-B and OX1 receptors. EXPERIMENTAL APPROACH The contribution of all orexin-B residues in orexin-B-induced apoptosis was investigated by alanine scanning. To determine which OX1 receptor domains are involved in orexin-B binding and apoptosis, a 3D model of OX1 receptor docked to the orexin-B C-terminus (AA-20-28) was developed. Substitution of residues present in OX1 receptor transmembrane (TM) domains by site-directed mutagenesis was performed. KEY RESULTS Alanine substitution of orexin-B residues, L(11) , L(15) , A(22) , G(24) , I(25) , L(26) and M(28) , altered orexin-B's binding affinity. Substitution of these residues and of the Q(16) , A(17) , S(18) , N(20) and T(27) residues inhibited apoptosis in CHO-S-OX1 receptor cells. The K(120) , P(123) , Y(124) , N(318) , K(321) , F(340) , T(341) , H(344) and W(345) residues localized in TM2, TM3, TM6 and TM7 of OX1 receptors were shown to play a role in orexin-B recognition and orexin-B/OX1 receptor-induced apoptosis. CONCLUSIONS AND IMPLICATIONS The C-terminus of orexin-B (i) plays an important role in its pro-apoptotic effect; and (ii) interacts with some residues localized in the OX1 receptor TM. This study defines the structure-function relationship for orexin-B recognition by human OX1 receptors and orexin-B/OX1 receptor-induced apoptosis, an important step for the future development of new agonist molecules.
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Affiliation(s)
- Pascal Nicole
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Pierre Couvineau
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Nadege Jamin
- Laboratoire des Protéines et Systèmes MembranairesCEA, iBiTecS, I2BCF‐91191Gif‐sur‐Yvette CedexFrance
| | - Thierry Voisin
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Alain Couvineau
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
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Heifetz A, Bodkin MJ, Biggin PC. Discovery of the First Selective, Nonpeptidic Orexin 2 Receptor Agonists. J Med Chem 2015; 58:7928-30. [PMID: 26375584 DOI: 10.1021/acs.jmedchem.5b01394] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this issue, Nagase and colleagues report the discovery of the first selective nonpeptidic orexin 2 receptor (OX2R) agonists. The discovery of these OX2R selective agonists opens up new avenues for therapies related to the activation of the orexin system, especially with respect to the treatment of sleep disorders such as narcolepsy.
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Affiliation(s)
- Alexander Heifetz
- Evotec (UK) Ltd. , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Mike J Bodkin
- Evotec (UK) 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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25
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Karhu L, Turku A, Xhaard H. Modeling of the OX1R-orexin-A complex suggests two alternative binding modes. BMC STRUCTURAL BIOLOGY 2015; 15:9. [PMID: 25957175 PMCID: PMC4469407 DOI: 10.1186/s12900-015-0036-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/21/2015] [Indexed: 01/25/2023]
Abstract
Background Interactions between the orexin peptides and their cognate OX1 and OX2 receptors remain poorly characterized. Site-directed mutagenesis studies on orexin peptides and receptors have indicated amino acids important for ligand binding and receptor activation. However, a better understanding of specific pairwise interactions would benefit small molecule discovery. Results We constructed a set of three-dimensional models of the orexin 1 receptor based on the 3D-structures of the orexin 2 receptor (released while this manuscript was under review), neurotensin receptor 1 and chemokine receptor CXCR4, conducted an exhaustive docking of orexin-A16–33 peptide fragment with ZDOCK and RDOCK, and analyzed a total of 4301 complexes through multidimensional scaling and clustering. The best docking poses reveal two alternative binding modes, where the C-terminus of the peptide lies deep in the binding pocket, on average about 5–6 Å above Tyr6.48 and close to Gln3.32. The binding modes differ in the about 100° rotation of the peptide; the peptide His26 faces either the receptor’s fifth transmembrane helix or the seventh helix. Both binding modes are well in line with previous mutation studies and partake in hydrogen bonding similar to suvorexant. Conclusions We present two binding modes for orexin-A into orexin 1 receptor, which help rationalize previous results from site-directed mutagenesis studies. The binding modes should serve small molecule discovery, and offer insights into the mechanism of receptor activation. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0036-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lasse Karhu
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Ainoleena Turku
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Henri Xhaard
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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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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Wozniak DR, Quinnell TG. Unmet needs of patients with narcolepsy: perspectives on emerging treatment options. Nat Sci Sleep 2015; 7:51-61. [PMID: 26045680 PMCID: PMC4447169 DOI: 10.2147/nss.s56077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The treatment options currently available for narcolepsy are often unsatisfactory due to suboptimal efficacy, troublesome side effects, development of drug tolerance, and inconvenience. Our understanding of the neurobiology of narcolepsy has greatly improved over the last decade. This knowledge has not yet translated into additional therapeutic options for patients, but progress is being made. Some compounds, such as histaminergic H3 receptor antagonists, may prove useful in symptom control of narcolepsy. The prospect of finding a cure still seems distant, but hypocretin replacement therapy offers some promise. In this narrative review, we describe these developments and others which may yield more effective narcolepsy treatments in the future.
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Affiliation(s)
- Dariusz R Wozniak
- Respiratory Support and Sleep Centre, Papworth Hospital, Cambridge, UK
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Cavasotto CN, Palomba D. Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun (Camb) 2015; 51:13576-94. [DOI: 10.1039/c5cc05050b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We show the key role of structural homology models in GPCR structure-based lead discovery and optimization, highlighting methodological aspects, recent progress and future directions.
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Affiliation(s)
- Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| | - Damián Palomba
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
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29
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Tautermann CS, Seeliger D, Kriegl JM. What can we learn from molecular dynamics simulations for GPCR drug design? Comput Struct Biotechnol J 2014; 13:111-21. [PMID: 25709761 PMCID: PMC4334948 DOI: 10.1016/j.csbj.2014.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 01/05/2023] Open
Abstract
Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this article we focus on the application of molecular dynamics (MD) simulations in GPCR drug discovery programs. Typical application scenarios of MD simulations and their scope and limitations will be described on the basis of two selected case studies, namely the binding of small molecule antagonists to the human CC chemokine receptor 3 (CCR3) and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3 (hM3R).
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Affiliation(s)
| | | | - Jan M. Kriegl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Support, Birkendorfer Str. 65, D-88397 Biberach a.d. Riss, Germany
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30
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A Structural Switch between Agonist and Antagonist Bound Conformations for a Ligand-Optimized Model of the Human Aryl Hydrocarbon Receptor Ligand Binding Domain. BIOLOGY 2014; 3:645-69. [PMID: 25329374 PMCID: PMC4280506 DOI: 10.3390/biology3040645] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/24/2014] [Accepted: 09/24/2014] [Indexed: 01/01/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that regulates the expression of a diverse group of genes. Exogenous AHR ligands include the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which is a potent agonist, and the synthetic AHR antagonist N-2-(1H-indol-3yl)ethyl)-9-isopropyl-2-(5-methylpyridin-3-yl)-9H-purin-6-amine (GNF351). As no experimentally determined structure of the ligand binding domain exists, homology models have been utilized for virtual ligand screening (VLS) to search for novel ligands. Here, we have developed an “agonist-optimized” homology model of the human AHR ligand binding domain, and this model aided in the discovery of two human AHR agonists by VLS. In addition, we performed molecular dynamics simulations of an agonist TCDD-bound and antagonist GNF351-bound version of this model in order to gain insights into the mechanics of the AHR ligand-binding pocket. These simulations identified residues 307–329 as a flexible segment of the AHR ligand pocket that adopts discrete conformations upon agonist or antagonist binding. This flexible segment of the AHR may act as a structural switch that determines the agonist or antagonist activity of a given AHR ligand.
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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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Abstract
Although narcolepsy was first described in the late nineteenth century in Germany and France, much of the research on this disorder has been conducted at Stanford University, starting with Drs. William C. Dement and Christian Guilleminault in the 1970s. The prevalence of narcolepsy was established, and a canine model discovered. Following the finding in Japan that almost all patients with narcolepsy carry a specific HLA subtype, HLA-DR2, Hugh Mac Devitt, F. Carl Grumet, and Larry Steinman initiated immunological studies, but results were generally negative. Using the narcoleptic canines, Dr. Nishino and I established that stimulants increased wakefulness by stimulating dopaminergic transmission while antidepressants suppress cataplexy via adrenergic reuptake inhibition. A linkage study was initiated with Dr. Grumet in 1988, and after 10 years of work, the canine narcolepsy gene was cloned by in 1999 and identified as the hypocretin (orexin) receptor 2. In 1992, studying African Americans, we also found that DQ0602 rather than DR2 was a better marker for narcolepsy across all ethnic groups. In 2000, Dr. Nishino and I, in collaboration with Dr. Lammers in the Netherlands, found that hypocretin 1 levels in the cerebrospinal fluid (CSF) were undetectable in most cases, establishing hypocretin deficiency as the cause of narcolepsy. Pursuing this research, our and Dr. Siegel's group, examining postmortem brains, found that the decreased CSF hypocretin 1 was secondary to the loss the 70,000 neurons producing hypocretin in the hypothalamus. This finding revived the autoimmune hypothesis but attempts at demonstrating immune targeting of hypocretin cells failed until 2013. At this date, Dr. Elisabeth Mellins and I discovered that narcolepsy is characterized by the presence of autoreactive CD4(+) T cells to hypocretin fragments when presented by DQ0602. Following reports that narcolepsy cases were triggered by vaccinations and infections against influenza A 2009 pH1N1, a new pandemic strain that erupted in 2009, our groups also established that a small epitope of pH1N1 resembles hypocretin and is likely involved in molecular mimicry. Although much remains to be done, these achievements, establishing hypocretin deficiency as the cause of narcolepsy, demonstrating its autoimmune basis, and showing molecular mimicry between hypocretin and sequences derived from a pandemic strain of influenza, are likely to remain classics in human immunology.
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Affiliation(s)
- Emmanuel J M Mignot
- Stanford University Center for Sleep Sciences, 3165 Porter Drive, #2178, Palo Alto, CA, 94304, USA,
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