De novo design of miniproteins targeting GPCRs
Abstract
G protein-coupled receptors (GPCRs) play key roles in physiology and are central targets for drug discovery and development1,2, but the design of protein agonists and antagonists has been challenging as GPCRs are integral membrane proteins and conformationally dynamic3–6. Here we describe computational de novo design methods and a high-throughput “receptor diversion” microscopy-based screen for generating GPCR binding miniproteins with high affinity, potency and selectivity. We design miniprotein agonists that activate receptors involved in itch and pain, as well as antagonists that inhibit receptors implicated in cancer, metabolic disorders such as diabetes and obesity, and migraine. Cryo-electron microscopy (cryo-EM) structures of five receptor-bound designs are close to the computational design models. A designed chemokine receptor antagonist mobilizes hematopoietic stem and progenitor cells in vivo at a level comparable to a clinically used drug, with fewer adverse effects.
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 52 print issues and online access
$199.00 per year
only $3.83 per issue
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
G protein-coupled receptors (GPCRs): advances in structures, mechanisms and drug discovery
Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery
Structure determination of inactive-state GPCRs with a universal nanobody
Author information
These authors contributed equally: Edin Muratspahić, David Feldman, David E. Kim, Xiangli Qu, Ana-Maria Bratovianu, Paula Rivera-Sánchez
Authors and Affiliations
Department of Biochemistry, University of Washington, Seattle, WA, USA
Edin Muratspahić, David Feldman, David E. Kim, Xiangli Qu, Isaac Sappington, Thomas Schlichthaerle, Jason Z. Zhang, Arvind Pillai, Brian Coventry, Ljubica Mihaljević, Magnus Bauer, Susana Vázquez Torres, Amir Motmaen, Gyu Rie Lee, Xinru Wang, Inna Goreshnik, Dionne K. Vafeados, Justin G. English, Lance Stewart, Christoffer Norn & David Baker
Institute for Protein Design, University of Washington, Seattle, WA, USA
Edin Muratspahić, David Feldman, David E. Kim, Xiangli Qu, Isaac Sappington, Thomas Schlichthaerle, Jason Z. Zhang, Arvind Pillai, Brian Coventry, Ljubica Mihaljević, Magnus Bauer, Susana Vázquez Torres, Amir Motmaen, Gyu Rie Lee, Long Tran, Xinru Wang, Inna Goreshnik, Dionne K. Vafeados, Justin G. English, Lance Stewart, Christoffer Norn & David Baker
BioInnovation Institute, Copenhagen N, Denmark
David Feldman, Ana-Maria Bratovianu, Paula Rivera-Sánchez, Federica Dimitri & Christoffer Norn
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
David E. Kim, Ljubica Mihaljević, Gyu Rie Lee & David Baker
Skape Bio ApS, Copenhagen N, Denmark
Ana-Maria Bratovianu, Paula Rivera-Sánchez, Jan Hendrik Voss, Emil P. T. Hertz, Mads Jeppesen, Amrita Nallathambi, Pia Peceli & Christoffer Norn
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Kensuke Sakamoto, Bryan L. Roth & Brian E. Krumm
NIMH Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
Kensuke Sakamoto, Bryan L. Roth & Brian E. Krumm
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
Jianjun Cao, Brian P. Cary, Matthew J. Belousoff, Peter Keov, Phuc N. H. Trinh, Patrick M. Sexton & Denise Wootten
ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
Jianjun Cao, Brian P. Cary, Matthew J. Belousoff, Peter Keov, Phuc N. H. Trinh, Patrick M. Sexton & Denise Wootten
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
Qingchao Chen, Yue Ren & Christopher G. Tate
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
Justyn Fine
Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA
Justyn Fine, Lauren Halloran & Jamie B. Spangler
Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
Sudha Mishra, Annu Dalal, Shachie Sinha, Ramanuj Banerjee, Manisankar Ganguly & Arun K. Shukla
University of Washington, Department of Medicine, Division of Medical Genetics, Seattle, WA, USA
Karthik Varappalayam Karuppusamy & André Lieber
Department of Chemical Engineering, University of Washington, Seattle, WA, USA
Long Tran
Department of Bioengineering, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA
Justin E. Svendsen & Parisa Hosseinzadeh
Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
Justin E. Svendsen & Parisa Hosseinzadeh
Novo Nordisk A/S, Måløv, Denmark
Nicolai Lindegaard, Matthäus Brandt, Yann Waltenspühl, Kristine Deibler, Lukas Deweid, Anja Bennett & Jendrik Schöppe
Novo Nordisk Research Centre China, Changping District, Beijing, China
Tiantang Dong & Xiaoli Yan
LeadHunter Services, Eurofins DiscoverX, LLC, Fremont, CA, USA
Luke Oostdyk, William Cao & Lakshmi Anantharaman
H. Lundbeck A/S, Global Research, Copenhagen-Valby, Denmark
Johan J. Weisser, Jesper Frank Bastlund, Christoffer Bundgaard & Ayodeji A. Asuni
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
Lauren Halloran & Jamie B. Spangler
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
Lauren Halloran & Jamie B. Spangler
- Edin Muratspahić
Search author on:PubMed Google Scholar
- David Feldman
Search author on:PubMed Google Scholar
- David E. Kim
Search author on:PubMed Google Scholar
- Xiangli Qu
Search author on:PubMed Google Scholar
- Ana-Maria Bratovianu
Search author on:PubMed Google Scholar
- Paula Rivera-Sánchez