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Dittman AH, May D, Johnson MA, Baldwin DH, Scholz NL. Odor exposure during imprinting periods increases odorant-specific sensitivity and receptor gene expression in coho salmon (Oncorhynchus kisutch). J Exp Biol 2024; 227:jeb247786. [PMID: 39238479 DOI: 10.1242/jeb.247786] [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: 04/17/2024] [Accepted: 08/23/2024] [Indexed: 09/07/2024]
Abstract
Pacific salmon are well known for their homing migrations; juvenile salmon learn odors associated with their natal streams prior to seaward migration, and then use these retained odor memories to guide them back from oceanic feeding grounds to their river of origin to spawn several years later. This memory formation, termed olfactory imprinting, involves (at least in part) sensitization of the peripheral olfactory epithelium to specific odorants. We hypothesized that this change in peripheral sensitivity is due to exposure-dependent increases in the expression of odorant receptor (OR) proteins that are activated by specific odorants experienced during imprinting. To test this hypothesis, we exposed juvenile coho salmon, Oncorhynchus kisutch, to the basic amino acid odorant l-arginine during the parr-smolt transformation (PST), when imprinting occurs, and assessed sensitivity of the olfactory epithelium to this and other odorants. We then identified the coho salmon ortholog of a basic amino acid odorant receptor (BAAR) and determined the mRNA expression levels of this receptor and other transcripts representing different classes of OR families. Exposure to l-arginine during the PST resulted in increased sensitivity to that odorant and a specific increase in BAAR mRNA expression in the olfactory epithelium relative to other ORs. These results suggest that specific increases in ORs activated during imprinting may be an important component of home stream memory formation and this phenomenon may ultimately be useful as a marker of successful imprinting to assess management strategies and hatchery practices that may influence straying in salmon.
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Affiliation(s)
- Andrew H Dittman
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd East, Seattle, WA 98112, USA
| | - Darran May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marc A Johnson
- Oregon Department of Fish and Wildlife Corvallis Research Laboratory, 28655 Highway 34, Corvallis, OR 97333, USA
| | - David H Baldwin
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd East, Seattle, WA 98112, USA
| | - Nathaniel L Scholz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd East, Seattle, WA 98112, USA
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Lalis M, Hladiš M, Abi Khalil S, Deroo C, Marin C, Bensafi M, Baldovini N, Briand L, Fiorucci S, Topin J. A status report on human odorant receptors and their allocated agonists. Chem Senses 2024; 49:bjae037. [PMID: 39400708 DOI: 10.1093/chemse/bjae037] [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: 03/12/2024] [Indexed: 10/15/2024] Open
Abstract
Olfactory perception begins when odorous substances interact with specialized receptors located on the surface of dedicated sensory neurons. The recognition of smells depends on a complex mechanism involving a combination of interactions between an odorant and a set of odorant receptors (ORs), where molecules are recognized according to a combinatorial activation code of ORs. Although these interactions have been studied for decades, the rules governing this ligand recognition remain poorly understood, and the complete combinatorial code is only known for a handful of odorants. We have carefully analyzed experimental results regarding the interactions between ORs and molecules to provide a status report on the deorphanization of ORs, i.e. the identification of the first agonist for a given sequence. This meticulous analysis highlights the influence of experimental methodology (cell line or readout) on molecule-receptor association results and shows that 83% of the results are conserved regardless of experimental conditions. The distribution of another key parameter, EC50, indicates that most OR ligand activities are in the micromolar range and that impurities could lead to erroneous conclusions. Focusing on the human ORs, our study shows that 88% of the documented sequences still need to be deorphanized. Finally, we also estimate the size of the ORs' recognition range, or broadness, as the number of odorants activating a given OR. By analogously estimating molecular broadness and combining the two estimates we propose a basic framework that can serve as a comparison point for future machine learning algorithms predicting OR-molecule activity.
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Affiliation(s)
- Maxence Lalis
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
| | - Matej Hladiš
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
| | - Samar Abi Khalil
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
| | - Christophe Deroo
- Expressions Parfumées, 136 chemin de St Marc, 06130, Grasse, France
| | - Christophe Marin
- Expressions Parfumées, 136 chemin de St Marc, 06130, Grasse, France
| | - Moustafa Bensafi
- Lyon Neuroscience Research Center, CNRS UMR 5292, INSERM U1028, University Claude Bernard Lyon, Bron, France
| | - Nicolas Baldovini
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000, Dijon, France
| | - Sébastien Fiorucci
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
| | - Jérémie Topin
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, Nice, France
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Bolnykh V, Rossetti G, Rothlisberger U, Carloni P. Expanding the boundaries of ligand–target modeling by exascale calculations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Viacheslav Bolnykh
- Laboratory of Computational Chemistry and Biochemistry École Polytechnique Fédérale de Lausanne Lausanne Switzerland
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM‐9)/Institute for Advanced Simulations (IAS‐5) Forschungszentrum Jülich Jülich Germany
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Neuroscience and Medicine (INM‐9)/Institute for Advanced Simulations (IAS‐5) Forschungszentrum Jülich Jülich Germany
- Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich Jülich Germany
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation University Hospital Aachen RWTH Aachen University Aachen Germany
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry École Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Paolo Carloni
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS‐5/INM‐9) “Computational Biomedicine” Forschungszentrum Jülich Jülich Germany
- JARA‐Institute INM‐11 “Molecular Neuroscience and Neuroimaging” Forschungszentrum Jülich Jülich Germany
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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Chia JSM, Wall ES, Wee CL, Rowland TAJ, Cheng RK, Cheow K, Guillemin K, Jesuthasan S. Bacteria evoke alarm behaviour in zebrafish. Nat Commun 2019; 10:3831. [PMID: 31444339 PMCID: PMC6707203 DOI: 10.1038/s41467-019-11608-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
When injured, fish release an alarm substance (Schreckstoff) that elicits fear in members of their shoal. Although Schreckstoff has been proposed to be produced by club cells in the skin, several observations indicate that these giant cells function primarily in immunity. Previous data indicate that the alarm substance can be isolated from mucus. Here we show that mucus, as well as bacteria, are transported from the external surface into club cells, by cytoplasmic transfer or invasion of cells, including neutrophils. The presence of bacteria inside club cells raises the possibility that the alarm substance may contain a bacterial component. Indeed, lysate from a zebrafish Staphylococcus isolate is sufficient to elicit alarm behaviour, acting in concert with a substance from fish. These results suggest that Schreckstoff, which allows one individual to unwittingly change the emotional state of the surrounding population, derives from two kingdoms and is associated with processes that protect the host from bacteria.
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Affiliation(s)
- Joanne Shu Ming Chia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Elena S Wall
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | | | - Thomas A J Rowland
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- St. Edmund Hall, University of Oxford, Oxford, UK
| | - Ruey-Kuang Cheng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Kathleen Cheow
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
| | - Suresh Jesuthasan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Singapore, Singapore.
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Selvam C, Lemasson IA, Brabet I, Oueslati N, Karaman B, Cabaye A, Tora AS, Commare B, Courtiol T, Cesarini S, McCort-Tranchepain I, Rigault D, Mony L, Bessiron T, McLean H, Leroux FR, Colobert F, Daniel H, Goupil-Lamy A, Bertrand HO, Goudet C, Pin JP, Acher FC. Increased Potency and Selectivity for Group III Metabotropic Glutamate Receptor Agonists Binding at Dual sites. J Med Chem 2018; 61:1969-1989. [DOI: 10.1021/acs.jmedchem.7b01438] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chelliah Selvam
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Isabelle A. Lemasson
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Isabelle Brabet
- IGF, CNRS, INSERM, Université Montpellier, F-34094 Montpellier, France
| | - Nadia Oueslati
- IGF, CNRS, INSERM, Université Montpellier, F-34094 Montpellier, France
| | - Berin Karaman
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Alexandre Cabaye
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Amélie S. Tora
- IGF, CNRS, INSERM, Université Montpellier, F-34094 Montpellier, France
| | - Bruno Commare
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- UMR 7509/CNRS/ECPM, Université de Strasbourg, 25 Rue Becquerel, 67087 Strasbourg 02, France
| | - Tiphanie Courtiol
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Sara Cesarini
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Isabelle McCort-Tranchepain
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Delphine Rigault
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Laetitia Mony
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Institut de Biologie, Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, PSL University, 46 rue d’Ulm, 75005 Paris, France
| | - Thomas Bessiron
- Pharmacologie et Biochimie de la Synapse, Université Paris-Sud/CNRS/NeuroPSI−UMR 9197, F-91405 Orsay, France
| | - Heather McLean
- Pharmacologie et Biochimie de la Synapse, Université Paris-Sud/CNRS/NeuroPSI−UMR 9197, F-91405 Orsay, France
| | - Frédéric R. Leroux
- UMR 7509/CNRS/ECPM, Université de Strasbourg, 25 Rue Becquerel, 67087 Strasbourg 02, France
| | - Françoise Colobert
- UMR 7509/CNRS/ECPM, Université de Strasbourg, 25 Rue Becquerel, 67087 Strasbourg 02, France
| | - Hervé Daniel
- Pharmacologie et Biochimie de la Synapse, Université Paris-Sud/CNRS/NeuroPSI−UMR 9197, F-91405 Orsay, France
| | - Anne Goupil-Lamy
- BIOVIA, Dassault Systèmes, 10 rue Marcel Dassault, CS 40501, 78946 Vélizy-Villacoublay Cedex, France
| | - Hugues-Olivier Bertrand
- BIOVIA, Dassault Systèmes, 10 rue Marcel Dassault, CS 40501, 78946 Vélizy-Villacoublay Cedex, France
| | - Cyril Goudet
- IGF, CNRS, INSERM, Université Montpellier, F-34094 Montpellier, France
| | - Jean-Philippe Pin
- IGF, CNRS, INSERM, Université Montpellier, F-34094 Montpellier, France
| | - Francine C. Acher
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
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7
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Claramunt RM, Santa María D, Alkorta I, Elguero J. The Structure ofN-phenyl-pyrazoles and Indazoles: Mononitro, Dinitro, and Trinitro Derivatives. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.3026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Rosa M. Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; UNED; Paseo Senda del Rey, 9 28040 Madrid Spain
| | - Dolores Santa María
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; UNED; Paseo Senda del Rey, 9 28040 Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Centro de Química Orgánica “Manuel Lora-Tamayo”; CSIC; Juan de la Cierva, 3 28006 Madrid Spain
| | - José Elguero
- Instituto de Química Médica, Centro de Química Orgánica “Manuel Lora-Tamayo”; CSIC; Juan de la Cierva, 3 28006 Madrid Spain
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Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein J Org Chem 2016; 12:2694-2718. [PMID: 28144341 PMCID: PMC5238551 DOI: 10.3762/bjoc.12.267] [Citation(s) in RCA: 317] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022] Open
Abstract
The process for drug discovery and development is challenging, time consuming and expensive. Computer-aided drug discovery (CADD) tools can act as a virtual shortcut, assisting in the expedition of this long process and potentially reducing the cost of research and development. Today CADD has become an effective and indispensable tool in therapeutic development. The human genome project has made available a substantial amount of sequence data that can be used in various drug discovery projects. Additionally, increasing knowledge of biological structures, as well as increasing computer power have made it possible to use computational methods effectively in various phases of the drug discovery and development pipeline. The importance of in silico tools is greater than ever before and has advanced pharmaceutical research. Here we present an overview of computational methods used in different facets of drug discovery and highlight some of the recent successes. In this review, both structure-based and ligand-based drug discovery methods are discussed. Advances in virtual high-throughput screening, protein structure prediction methods, protein-ligand docking, pharmacophore modeling and QSAR techniques are reviewed.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
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Montagné N, de Fouchier A, Newcomb RD, Jacquin-Joly E. Advances in the identification and characterization of olfactory receptors in insects. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 130:55-80. [PMID: 25623337 DOI: 10.1016/bs.pmbts.2014.11.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Olfactory receptors (ORs) are the key elements of the molecular machinery responsible for the detection of odors in insects. Since their initial discovery in Drosophila melanogaster at the beginning of the twenty-first century, insect ORs have been the focus of intense research, both for fundamental knowledge of sensory systems and for their potential as novel targets for the development of products that could impact harmful behaviors of crop pests and disease vectors. In recent years, studies on insect ORs have entered the genomic era, with an ever-increasing number of OR genes being characterized every year through the sequencing of genomes and transcriptomes. With the upcoming release of genomic sequences from hundreds of insect species, the insect OR family could very well become the largest multigene family known. This extremely rapid identification of ORs in many insects is driving the necessity for the development of high-throughput technologies that will allow the identification of ligands for this unprecedented number of receptors. Moreover, such technologies will also be important for the development of agonists or antagonists that could be used in the fight against pest insects.
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Affiliation(s)
- Nicolas Montagné
- Institute of Ecology & Environmental Sciences of Paris, UPMC-Sorbonne Universités, Paris, France
| | - Arthur de Fouchier
- Institute of Ecology & Environmental Sciences of Paris, INRA, Versailles, France
| | - Richard D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
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Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest ARR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C, Carninci P, Gustincich S. Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics 2014; 15:729. [PMID: 25164183 PMCID: PMC4161876 DOI: 10.1186/1471-2164-15-729] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 08/18/2014] [Indexed: 01/15/2023] Open
Abstract
Background The mesencephalic dopaminergic (mDA) cell system is composed of two major groups of projecting cells in the Substantia Nigra (SN) (A9 neurons) and the Ventral Tegmental Area (VTA) (A10 cells). Selective degeneration of A9 neurons occurs in Parkinson’s disease (PD) while abnormal function of A10 cells has been linked to schizophrenia, attention deficit and addiction. The molecular basis that underlies selective vulnerability of A9 and A10 neurons is presently unknown. Results By taking advantage of transgenic labeling, laser capture microdissection coupled to nano Cap-Analysis of Gene Expression (nanoCAGE) technology on isolated A9 and A10 cells, we found that a subset of Olfactory Receptors (OR)s is expressed in mDA neurons. Gene expression analysis was integrated with the FANTOM5 Helicos CAGE sequencing datasets, showing the presence of these ORs in selected tissues and brain areas outside of the olfactory epithelium. OR expression in the mesencephalon was validated by RT-PCR and in situ hybridization. By screening 16 potential ligands on 5 mDA ORs recombinantly expressed in an heterologous in vitro system, we identified carvone enantiomers as agonists at Olfr287 and able to evoke an intracellular Ca2+ increase in solitary mDA neurons. ORs were found expressed in human SN and down-regulated in PD post mortem brains. Conclusions Our study indicates that mDA neurons express ORs and respond to odor-like molecules providing new opportunities for pharmacological intervention in disease. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-729) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Piero Carninci
- SISSA, Area of Neuroscience, via Bonomea 265, 34136 Trieste, Italy.
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From Three-Dimensional GPCR Structure to Rational Ligand Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:129-57. [DOI: 10.1007/978-94-007-7423-0_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.
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Affiliation(s)
- Gregory Sliwoski
- Jr., Center for Structural Biology, 465 21st Ave South, BIOSCI/MRBIII, Room 5144A, Nashville, TN 37232-8725.
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Activation of olfactory receptors on mouse pulmonary macrophages promotes monocyte chemotactic protein-1 production. PLoS One 2013; 8:e80148. [PMID: 24278251 PMCID: PMC3836993 DOI: 10.1371/journal.pone.0080148] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/29/2013] [Indexed: 12/31/2022] Open
Abstract
Background Emerging evidence suggests that non-olfactory tissues and cells can express olfactory receptors (ORs), however, the exact function of ectopic OR expression remains unknown. We have previously shown in mouse models that a unique cooperation between interferon-γ (IFN-γ) and lipopolysaccharide (LPS) drives the activation of pulmonary macrophages and leads to the induction of pathogenic responses in the respiratory tract. Further, through gene array studies, we have shown that activation of macrophages by these molecules results in the selective expression of a number of ORs. In this study, we validated the expression of these ORs in mouse airway and pulmonary macrophages in response to IFN-γ and LPS (γ/LPS) stimulation, and further explored the effect of odorant stimulation on macrophage function. Methodology/Principal Findings OR expression in airway and pulmonary macrophages in response to IFN-γ, LPS or γ/LPS treatments was assessed by microarray and validated by q-PCR. OR expression (e.g. OR622) on macrophages was confirmed by visualization in immunofluoresence assays. Functional responses to odorants were assessed by quantifying inflammatory cytokine and chemokine expression using q-PCR and cell migration was assessed by a modified Boyden chamber migration assay. Our results demonstrate that eight ORs are expressed at basal levels in both airway and pulmonary macrophages, and that γ/LPS stimulation cooperatively increased this expression. Pulmonary macrophages exposed to the combined treatment of γ/LPS+octanal (an odorant) exhibited a 3-fold increase in MCP-1 protein production, compared to cells treated with γ/LPS alone. Supernatants from γ/LPS+octanal exposed macrophages also increased macrophage migration in vitro. Conclusions/Significance Eight different ORs are expressed at basal levels in pulmonary macrophages and expression is upregulated by the synergistic action of γ/LPS. Octanal stimulation further increased MCP-1 production and the motility of macrophages. Our results suggest that ORs may mediate macrophage function by regulating MCP-1 production and cell migration.
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Boyle SM, McInally S, Ray A. Expanding the olfactory code by in silico decoding of odor-receptor chemical space. eLife 2013; 2:e01120. [PMID: 24137542 PMCID: PMC3787389 DOI: 10.7554/elife.01120] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/26/2013] [Indexed: 01/30/2023] Open
Abstract
Coding of information in the peripheral olfactory system depends on two fundamental factors: interaction of individual odors with subsets of the odorant receptor repertoire and mode of signaling that an individual receptor-odor interaction elicits, activation or inhibition. We develop a cheminformatics pipeline that predicts receptor–odorant interactions from a large collection of chemical structures (>240,000) for receptors that have been tested to a smaller panel of odorants (∼100). Using a computational approach, we first identify shared structural features from known ligands of individual receptors. We then use these features to screen in silico new candidate ligands from >240,000 potential volatiles for several Odorant receptors (Ors) in the Drosophila antenna. Functional experiments from 9 Ors support a high success rate (∼71%) for the screen, resulting in identification of numerous new activators and inhibitors. Such computational prediction of receptor–odor interactions has the potential to enable systems level analysis of olfactory receptor repertoires in organisms. DOI:http://dx.doi.org/10.7554/eLife.01120.001 Although our sense of smell is regarded as inferior to that of many other species, we can nevertheless distinguish between roughly 10,000 different odors. These are made up of molecules called odorants, each of which activates a specific subset of odorant receptors in the nose. However, much of what we know about this process has come from studying the fruit fly, Drosophila, which detects odors using receptors located mainly on its antennae. The number of potential odorants in nature is vast, and only a tiny fraction of the interactions between odorants and receptors can be physically tested. To address this challenge, Boyle et al. have used a computational approach to study in depth the interactions between a subset of 24 odorant receptors in Drosophila antennae and 109 odorants. After developing a method to identify structural features shared by the odorants that activate each receptor, Boyle et al. used this information to perform a computational (in silico) screen of more than 240,000 different odorant-like volatile compounds. For each receptor, they compiled a list of the 500 odorants predicted to interact most strongly with it. They then tested their predictions for a subset of the receptors by performing experiments in living flies, and found that roughly 71% of predicted compounds did indeed activate or inhibit their receptors, compared to only 10% of a control sample. In addition to providing new insights into the nature of the interactions between odorants and their receptors, the computational screen devised by Boyle et al. could aid the development of novel insect repellents, or compounds that mask the odors used by disease-causing insects to identify their hosts. It could also be used in the future to develop novel flavors and fragrances. DOI:http://dx.doi.org/10.7554/eLife.01120.002
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Affiliation(s)
- Sean Michael Boyle
- Genetics, Genomics, and Bioinformatics Program , University of California, Riverside , Riverside , United States
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Alkorta I, Cossío FP, Elguero J, Fresno N, Hernandez-Folgado L, García-Granda S, Menéndez-Taboada L, Pérez-Fernández R, Reviriego F, Vázquez-Viñuela L. The reaction of NH-indazoles with 1-fluoro-2,4-dinitrobenzene: the unusual formation of benzotriazole-N-oxides. NEW J CHEM 2013. [DOI: 10.1039/c3nj00186e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gelis L, Wolf S, Hatt H, Neuhaus EM, Gerwert K. Vorhersage der Ligandenerkennung in einem Geruchsrezeptor durch Kombination von ortsgerichteter Mutagenese und dynamischer Homologie-Modellierung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103980] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Gelis L, Wolf S, Hatt H, Neuhaus EM, Gerwert K. Prediction of a ligand-binding niche within a human olfactory receptor by combining site-directed mutagenesis with dynamic homology modeling. Angew Chem Int Ed Engl 2011; 51:1274-8. [PMID: 22144177 DOI: 10.1002/anie.201103980] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 10/10/2011] [Indexed: 01/28/2023]
Affiliation(s)
- Lian Gelis
- Lehrstuhl für Zellphysiologie, Ruhr-University Bochum, Germany
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Family structure and phylogenetic analysis of odorant receptor genes in the large yellow croaker (Larimichthys crocea). BMC Evol Biol 2011; 11:237. [PMID: 21834959 PMCID: PMC3162931 DOI: 10.1186/1471-2148-11-237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 08/11/2011] [Indexed: 12/14/2022] Open
Abstract
Background Chemosensory receptors, which are all G-protein-coupled receptors (GPCRs), come in four types: odorant receptors (ORs), vomeronasal receptors, trace-amine associated receptors and formyl peptide receptor-like proteins. The ORs are the most important receptors for detecting a wide range of environmental chemicals in daily life. Most fish OR genes have been identified from genome databases following the completion of the genome sequencing projects of many fishes. However, it remains unclear whether these OR genes from the genome databases are actually expressed in the fish olfactory epithelium. Thus, it is necessary to clone the OR mRNAs directly from the olfactory epithelium and to examine their expression status. Results Eighty-nine full-length and 22 partial OR cDNA sequences were isolated from the olfactory epithelium of the large yellow croaker, Larimichthys crocea. Bayesian phylogenetic analysis classified the vertebrate OR genes into two types, with several clades within each type, and showed that the L. crocea OR genes of each type are more closely related to those of fugu, pufferfish and stickleback than they are to those of medaka, zebrafish and frog. The reconciled tree showed 178 duplications and 129 losses. The evolutionary relationships among OR genes in these fishes accords with their evolutionary history. The fish OR genes have experienced functional divergence, and the different clades of OR genes have evolved different functions. The result of real-time PCR shows that different clades of ORs have distinct expression levels. Conclusion We have shown about 100 OR genes to be expressed in the olfactory epithelial tissues of L. crocea. The OR genes of modern fishes duplicated from their common ancestor, and were expanded over evolutionary time. The OR genes of L. crocea are closely related to those of fugu, pufferfish and stickleback, which is consistent with its evolutionary position. The different expression levels of OR genes of large yellow croaker may suggest varying roles of ORs in olfactory function.
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Ma DL, Chan DSH, Leung CH. Molecular docking for virtual screening of natural product databases. Chem Sci 2011. [DOI: 10.1039/c1sc00152c] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Mony L, Triballeau N, Paoletti P, Acher FC, Bertrand HO. Identification of a novel NR2B-selective NMDA receptor antagonist using a virtual screening approach. Bioorg Med Chem Lett 2010; 20:5552-8. [DOI: 10.1016/j.bmcl.2010.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/09/2010] [Accepted: 07/09/2010] [Indexed: 12/01/2022]
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Massa SM, Yang T, Xie Y, Shi J, Bilgen M, Joyce JN, Nehama D, Rajadas J, Longo FM. Small molecule BDNF mimetics activate TrkB signaling and prevent neuronal degeneration in rodents. J Clin Invest 2010; 120:1774-85. [PMID: 20407211 DOI: 10.1172/jci41356] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 02/17/2010] [Indexed: 02/01/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) activates the receptor tropomyosin-related kinase B (TrkB) with high potency and specificity, promoting neuronal survival, differentiation, and synaptic function. Correlations between altered BDNF expression and/or function and mechanism(s) underlying numerous neurodegenerative conditions, including Alzheimer disease and traumatic brain injury, suggest that TrkB agonists might have therapeutic potential. Using in silico screening with a BDNF loop-domain pharmacophore, followed by low-throughput in vitro screening in mouse fetal hippocampal neurons, we have efficiently identified small molecules with nanomolar neurotrophic activity specific to TrkB versus other Trk family members. Neurotrophic activity was dependent on TrkB and its downstream targets, although compound-induced signaling activation kinetics differed from those triggered by BDNF. A selected prototype compound demonstrated binding specificity to the extracellular domain of TrkB. In in vitro models of neurodegenerative disease, it prevented neuronal degeneration with efficacy equal to that of BDNF, and when administered in vivo, it caused hippocampal and striatal TrkB activation in mice and improved motor learning after traumatic brain injury in rats. These studies demonstrate the utility of loop modeling in drug discovery and reveal what we believe to be the first reported small molecules derived from a targeted BDNF domain that specifically activate TrkB.We propose that these compounds constitute a novel group of tools for the study of TrkB signaling and may provide leads for developing new therapeutic agents for neurodegenerative diseases.
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Affiliation(s)
- Stephen M Massa
- Department of Neurology and Laboratory for Computational Neurochemistry and Drug Discovery, UCSF, San Francisco, California, USA
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