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3. Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

Author

Camillo Rosano, Jie Xia, David Rodriguez, Manuel Pastor, Stefano Moro, Ajit Jadhav, Balaji Selvam, Sebastien Fiorucci, Ingebrigt Sylte, Serge Antonczak, Vsevolod Katritch, Serdar Durdagi, Ki Chul Park, Gerard Van Westen, Henri Xhaard, Raymond Stevens, Jiye Shi, Philip Biggin, Davide Sabbadin, SHUGUANG YUAN, Slawomir Filipek, David Gloriam, Antonella Ciancetta, Marek Bajda, Supriyo Bhattacharya, Hahnbeom Park, Jens Carlsson, Aleksandrs Gutcaits, Bartosz Trzaskowski, Jianyi Yang, William Pitt, Dorota Latek, Liliana Halip, Elizabeth Nguyen, Irina Kufareva, Noel Southall, Joaquin Ambia, Woong-Hee Shin, Jana Selent, Uddhavesh Sonavane, Marco Ponassi, Julien Diharce, Jose Manuel Perez-Aguilar, Nicos Petasis, Sergei Grudinin, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Department of Molecular Biology [San Diego], The Scripps Research Institute [La Jolla], University of California-University of California-University of California [San Diego] (UC San Diego), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Université Joseph Fourier - Grenoble 1 (UJF)-Université Pierre Mendès France - Grenoble 2 (UPMF), Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of California (UC)-University of California (UC), The Scripps Research Institute [La Jolla, San Diego], Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])

Subjects
Models, Molecular, Protein Conformation, Bioinformatics, 01 natural sciences, Molecular Docking Simulation, Receptors, G-Protein-Coupled, Protein structure, Ligand docking, Models, Structural Biology, Receptors, 0303 health sciences, Crystallography, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Homology modeling, Biological Sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Smoothened Receptor, Structure-based drug discovery, Protein Binding, Serotonin, 1.1 Normal biological development and functioning, Allosteric regulation, Biophysics, Computational biology, Biology, 010402 general chemistry, Article, G-Protein-Coupled, 03 medical and health sciences, Underpinning research, Information and Computing Sciences, DOCK, Structure prediction, Humans, Molecular Biology, 030304 developmental biology, G protein-coupled receptor, Conformational sampling, Pharmacology, Participants of GPCR Dock 2013, Binding Sites, Molecular, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 0104 chemical sciences, Docking (molecular), Receptors, Serotonin, Chemical Sciences, G-protein coupled receptor, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Generic health relevance, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.

Published
2014
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4. Maresin-1 regulates type 2 innate lymphoid cells and promotes generation of regulatory T cells to limit allergic inflammation (HYP2P.336)

Author

Nandini Krishnamoorthy, Patrick Burkett, Jessmond Dalli, Raja-Elie Abdulnour, Romain Colas, Sesquile Ramon, Richard Phipps, Nicos Petasis, Vijay Kuchroo, Charles Serhan, and Bruce Levy

Subjects
Immunology, Immunology and Allergy
Abstract

Asthma is a chronic inflammatory disease that fails to resolve and is classically considered to be mediated by an overzealous CD4+Th2 immune response. Recently, a key role for type 2 innate lymphoid cells (ILC2s) was shown to have an important role in the initiation and amplification of allergic inflammation; however, mechanisms for ILC2 regulation remain to be determined. In this study, metabololipidomics of murine lungs identified temporal changes in the endogenous levels of docosahexaenoic acid (DHA)-derived pro-resolving mediator, maresin 1, (MaR1) during self-limited allergic inflammation to ovalbumin (OVA). MaR1 decreased after allergen challenge relative to levels found during sensitization, and subsequently increased during the resolution of inflammation. Exogenous administration of MaR1 reduced lung inflammation and ILC2 expression of IL-5 and IL-13 and increased amphiregulin. MaR1 augmented de novo generation of regulatory T cells (Tregs), which interacted with ILC2s to markedly suppress cytokine production in a TGF-β-dependent manner. Antibody-mediated depletion of Tregs interrupted MaR1 control of ILC2 expression of IL-13 in vivo. These results point to a pivotal role for Tregs in the control of ILC2s in a new proresolving mechanism engaged by MaR1.

Published
2015
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