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Lyapina E, Marin E, Gusach A, Orekhov P, Gerasimov A, Luginina A, Vakhrameev D, Ergasheva M, Kovaleva M, Khusainov G, Khorn P, Shevtsov M, Kovalev K, Bukhdruker S, Okhrimenko I, Popov P, Hu H, Weierstall U, Liu W, Cho Y, Gushchin I, Rogachev A, Bourenkov G, Park S, Park G, Hyun HJ, Park J, Gordeliy V, Borshchevskiy V, Mishin A, Cherezov V. Structural basis for receptor selectivity and inverse agonism in S1P 5 receptors. Nat Commun 2022; 13:4736. [PMID: 35961984 PMCID: PMC9374744 DOI: 10.1038/s41467-022-32447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.
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Affiliation(s)
- Elizaveta Lyapina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Egor Marin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Anastasiia Gusach
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Philipp Orekhov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, 518172, China
| | | | - Aleksandra Luginina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Daniil Vakhrameev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Margarita Ergasheva
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Margarita Kovaleva
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Georgii Khusainov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- Division of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, PSI, Switzerland
| | - Polina Khorn
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Mikhail Shevtsov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Kirill Kovalev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Sergey Bukhdruker
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Ivan Okhrimenko
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Petr Popov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- iMolecule, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, 85281, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ, 85281, USA
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ivan Gushchin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Andrey Rogachev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
- Joint Institute for Nuclear Research, Dubna, 141980, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Hyo Jung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, POSTECH, Pohang, 37673, Republic of Korea
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38400, France
| | - Valentin Borshchevskiy
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
- Joint Institute for Nuclear Research, Dubna, 141980, Russia.
| | - Alexey Mishin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.
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