IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37041-7.html
   My bibliography  Save this article

Molecular mechanism of biased signaling at the kappa opioid receptor

Author

Listed:
  • Amal El Daibani

    (Washington University School of Medicine
    University of Health Sciences & Pharmacy and Washington University School of Medicine)

  • Joseph M. Paggi

    (Stanford University)

  • Kuglae Kim

    (University of North Carolina School of Medicine
    Yonsei University)

  • Yianni D. Laloudakis

    (Stanford University)

  • Petr Popov

    (iMolecule, Skolkovo Institute of Science and Technology)

  • Sarah M. Bernhard

    (Washington University School of Medicine
    University of Health Sciences & Pharmacy and Washington University School of Medicine)

  • Brian E. Krumm

    (University of North Carolina School of Medicine)

  • Reid H. J. Olsen

    (University of North Carolina School of Medicine)

  • Jeffrey Diberto

    (University of North Carolina School of Medicine)

  • F. Ivy Carroll

    (Research Triangle Institute)

  • Vsevolod Katritch

    (University of Southern California)

  • Bernhard Wünsch

    (Universität Münster)

  • Ron O. Dror

    (Stanford University
    Stanford University School of Medicine)

  • Tao Che

    (Washington University School of Medicine
    University of Health Sciences & Pharmacy and Washington University School of Medicine)

Abstract

The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.

Suggested Citation

  • Amal El Daibani & Joseph M. Paggi & Kuglae Kim & Yianni D. Laloudakis & Petr Popov & Sarah M. Bernhard & Brian E. Krumm & Reid H. J. Olsen & Jeffrey Diberto & F. Ivy Carroll & Vsevolod Katritch & Bern, 2023. "Molecular mechanism of biased signaling at the kappa opioid receptor," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37041-7
    DOI: 10.1038/s41467-023-37041-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37041-7
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37041-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Dean P. Staus & Hongli Hu & Michael J. Robertson & Alissa L. W. Kleinhenz & Laura M. Wingler & William D. Capel & Naomi R. Latorraca & Robert J. Lefkowitz & Georgios Skiniotis, 2020. "Structure of the M2 muscarinic receptor–β-arrestin complex in a lipid nanodisc," Nature, Nature, vol. 579(7798), pages 297-302, March.
    2. Tao Che & Justin English & Brian E. Krumm & Kuglae Kim & Els Pardon & Reid H. J. Olsen & Sheng Wang & Shicheng Zhang & Jeffrey F. Diberto & Noah Sciaky & F. Ivy Carroll & Jan Steyaert & Daniel Wacker , 2020. "Nanobody-enabled monitoring of kappa opioid receptor states," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. Weijiao Huang & Matthieu Masureel & Qianhui Qu & John Janetzko & Asuka Inoue & Hideaki E. Kato & Michael J. Robertson & Khanh C. Nguyen & Jeffrey S. Glenn & Georgios Skiniotis & Brian K. Kobilka, 2020. "Structure of the neurotensin receptor 1 in complex with β-arrestin 1," Nature, Nature, vol. 579(7798), pages 303-308, March.
    4. Naomi R. Latorraca & Jason K. Wang & Brian Bauer & Raphael J. L. Townshend & Scott A. Hollingsworth & Julia E. Olivieri & H. Eric Xu & Martha E. Sommer & Ron O. Dror, 2018. "Molecular mechanism of GPCR-mediated arrestin activation," Nature, Nature, vol. 557(7705), pages 452-456, May.
    5. Aashish Manglik & Henry Lin & Dipendra K. Aryal & John D. McCorvy & Daniela Dengler & Gregory Corder & Anat Levit & Ralf C. Kling & Viachaslau Bernat & Harald Hübner & Xi-Ping Huang & Maria F. Sassano, 2016. "Structure-based discovery of opioid analgesics with reduced side effects," Nature, Nature, vol. 537(7619), pages 185-190, September.
    6. Sheng Wang & Tao Che & Anat Levit & Brian K. Shoichet & Daniel Wacker & Bryan L. Roth, 2018. "Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone," Nature, Nature, vol. 555(7695), pages 269-273, March.
    7. Andreas Bock & Nicole Merten & Ramona Schrage & Clelia Dallanoce & Julia Bätz & Jessica Klöckner & Jens Schmitz & Carlo Matera & Katharina Simon & Anna Kebig & Lucas Peters & Anke Müller & Jasmin Schr, 2012. "The allosteric vestibule of a seven transmembrane helical receptor controls G-protein coupling," Nature Communications, Nature, vol. 3(1), pages 1-11, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Andrew J. Y. Jones & Thomas H. Harman & Matthew Harris & Oliver E. Lewis & Graham Ladds & Daniel Nietlispach, 2024. "Binding kinetics drive G protein subtype selectivity at the β1-adrenergic receptor," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Raphael S. Haider & Edda S. F. Matthees & Julia Drube & Mona Reichel & Ulrike Zabel & Asuka Inoue & Andy Chevigné & Cornelius Krasel & Xavier Deupi & Carsten Hoffmann, 2022. "β-arrestin1 and 2 exhibit distinct phosphorylation-dependent conformations when coupling to the same GPCR in living cells," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Junke Liu & Hengmin Tang & Chanjuan Xu & Shengnan Zhou & Xunying Zhu & Yuanyuan Li & Laurent Prézeau & Tao Xu & Jean-Philippe Pin & Philippe Rondard & Wei Ji & Jianfeng Liu, 2022. "Biased signaling due to oligomerization of the G protein-coupled platelet-activating factor receptor," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Yutaro Shiraishi & Yutaka Kofuku & Takumi Ueda & Shubhi Pandey & Hemlata Dwivedi-Agnihotri & Arun K. Shukla & Ichio Shimada, 2021. "Biphasic activation of β-arrestin 1 upon interaction with a GPCR revealed by methyl-TROSY NMR," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    4. Pankaj Sharma & Elena Maklashina & Markus Voehler & Sona Balintova & Sarka Dvorakova & Michal Kraus & Katerina Hadrava Vanova & Zuzana Nahacka & Renata Zobalova & Stepana Boukalova & Kristyna Cunatova, 2024. "Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Xiao Teng & Sijia Chen & Yingying Nie & Peng Xiao & Xiao Yu & Zhenhua Shao & Sanduo Zheng, 2022. "Ligand recognition and biased agonism of the D1 dopamine receptor," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Yong-Seok Kim & Jun-Hee Yeon & Woori Ko & Byung-Chang Suh, 2023. "Two-step structural changes in M3 muscarinic receptor activation rely on the coupled Gq protein cycle," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    7. Yosuke Toyoda & Angqi Zhu & Fang Kong & Sisi Shan & Jiawei Zhao & Nan Wang & Xiaoou Sun & Linqi Zhang & Chuangye Yan & Brian K. Kobilka & Xiangyu Liu, 2023. "Structural basis of α1A-adrenergic receptor activation and recognition by an extracellular nanobody," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Yasmin Aydin & Thore Böttke & Jordy Homing Lam & Stefan Ernicke & Anna Fortmann & Maik Tretbar & Barbara Zarzycka & Vsevolod V. Gurevich & Vsevolod Katritch & Irene Coin, 2023. "Structural details of a Class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    9. Lin Cheng & Zhuang Miao & Sicen Liu & Zhe Li & Hong Fu & Chanjuan Xu & Shilong Hu & Chang Zhao & Yuxuan Liu & Tiantian Zhao & Wencheng Liu & Heli Wang & Runduo Liu & Wei Yan & Xiangdong Tang & Jianfen, 2024. "Cryo-EM structure of small-molecule agonist bound delta opioid receptor-Gi complex enables discovery of biased compound," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Björn D. M. Bean & Colleen J. Mulvihill & Riddhiman K. Garge & Daniel R. Boutz & Olivier Rousseau & Brendan M. Floyd & William Cheney & Elizabeth C. Gardner & Andrew D. Ellington & Edward M. Marcotte , 2022. "Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    11. Fabian Bumbak & James B. Bower & Skylar C. Zemmer & Asuka Inoue & Miquel Pons & Juan Carlos Paniagua & Fei Yan & James Ford & Hongwei Wu & Scott A. Robson & Ross A. D. Bathgate & Daniel J. Scott & Pau, 2023. "Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    12. Mithu Baidya & Madhu Chaturvedi & Hemlata Dwivedi-Agnihotri & Ashutosh Ranjan & Dominic Devost & Yoon Namkung & Tomasz Maciej Stepniewski & Shubhi Pandey & Minakshi Baruah & Bhanupriya Panigrahi & Par, 2022. "Allosteric modulation of GPCR-induced β-arrestin trafficking and signaling by a synthetic intrabody," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    13. Dylan Scott Eiger & Noelia Boldizsar & Christopher Cole Honeycutt & Julia Gardner & Stephen Kirchner & Chloe Hicks & Issac Choi & Uyen Pham & Kevin Zheng & Anmol Warman & Jeffrey S. Smith & Jennifer Y, 2022. "Location bias contributes to functionally selective responses of biased CXCR3 agonists," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    14. Justine S. Paradis & Xiang Feng & Brigitte Murat & Robert E. Jefferson & Badr Sokrat & Martyna Szpakowska & Mireille Hogue & Nick D. Bergkamp & Franziska M. Heydenreich & Martine J. Smit & Andy Chevig, 2022. "Computationally designed GPCR quaternary structures bias signaling pathway activation," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. Ruibo Zhai & Zhuoqi Wang & Zhaofei Chai & Xiaogang Niu & Conggang Li & Changwen Jin & Yunfei Hu, 2023. "Distinct activation mechanisms of β-arrestin-1 revealed by 19F NMR spectroscopy," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    16. Kouki Kawakami & Masataka Yanagawa & Suzune Hiratsuka & Misaki Yoshida & Yuki Ono & Michio Hiroshima & Masahiro Ueda & Junken Aoki & Yasushi Sako & Asuka Inoue, 2022. "Heterotrimeric Gq proteins act as a switch for GRK5/6 selectivity underlying β-arrestin transducer bias," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    17. Sandra Arroyo-Urea & Antonina L. Nazarova & Ángela Carrión-Antolí & Alessandro Bonifazi & Francisco O. Battiti & Jordy Homing Lam & Amy Hauck Newman & Vsevolod Katritch & Javier García-Nafría, 2024. "A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    18. Alexa Strauss & Alberto J. Gonzalez-Hernandez & Joon Lee & Nohely Abreu & Purushotham Selvakumar & Leslie Salas-Estrada & Melanie Kristt & Anisul Arefin & Kevin Huynh & Dagan C. Marx & Kristen Gillila, 2024. "Structural basis of positive allosteric modulation of metabotropic glutamate receptor activation and internalization," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    19. T. Bertie Ansell & Wanling Song & Claire E. Coupland & Loic Carrique & Robin A. Corey & Anna L. Duncan & C. Keith Cassidy & Maxwell M. G. Geurts & Tim Rasmussen & Andrew B. Ward & Christian Siebold & , 2023. "LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    20. Jun Yu & Amit Kumar & Xuefeng Zhang & Charlotte Martin & Kevin Van holsbeeck & Pierre Raia & Antoine Koehl & Toon Laeremans & Jan Steyaert & Aashish Manglik & Steven Ballet & Andreas Boland & Miriam S, 2024. "Structural basis of μ-opioid receptor targeting by a nanobody antagonist," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37041-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.