De-novo macrocyclic peptides dissect energy coupling of a heterodimeric ABC transporter by multimode allosteric inhibition

  1. Erich Stefan
  2. Richard Obexer
  3. Susanne Hofmann
  4. Khanh Vu Huu
  5. Yichao Huang
  6. Nina Morgner
  7. Hiroaki Suga  Is a corresponding author
  8. Robert Tampé  Is a corresponding author
  1. Goethe University Frankfurt, Germany
  2. The University of Tokyo, Japan

Abstract

ATP-binding cassette (ABC) transporters constitute the largest family of primary active transporters involved in a multitude of physiological processes and human diseases. Despite considerable efforts, it remains unclear how ABC transporters harness the chemical energy of ATP to drive substrate transport across cell membranes. Here, by random nonstandard peptide integrated discovery (RaPID), we leveraged combinatorial macrocyclic peptides that target a heterodimeric ABC transport complex and explore fundamental principles of the substrate translocation cycle. High-affinity peptidic macrocycles bind conformationally selective and display potent multimode inhibitory effects. The macrocycles block the transporter either before or after unidirectional substrate export along a single conformational switch induced by ATP binding. Our study reveals mechanistic principles of ATP binding, conformational switching, and energy transduction for substrate transport of ABC export systems. We highlight the potential of de novo macrocycles as effective inhibitors for membrane proteins implicated in multidrug resistance, providing avenues for the next-generation of pharmaceuticals.

Data availability

All data denerated or analyzed during this study are included in the manuscript and support files. A source data file has been provided for Figure 1C (Sequencing Data), Figure 2-6, Figure 2-supplement figure 1,and Figure 5-supplement figure 1.

Article and author information

Author details

  1. Erich Stefan

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Richard Obexer

    Department of Chemistry, The University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  3. Susanne Hofmann

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Khanh Vu Huu

    3Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Yichao Huang

    Department of Chemistry, The University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. Nina Morgner

    Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1872-490X
  7. Hiroaki Suga

    Department of Chemistry, The University of Tokyo, Tokyo, Japan
    For correspondence
    hsuga@chem.su-tokyo.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
  8. Robert Tampé

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
    For correspondence
    tampe@em.uni-frankfurt.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0403-2160

Funding

Deutsche Forschungsgemeinschaft (TA 157/12-1)

  • Robert Tampé

Deutsche Forschungsgemeinschaft (CRC 807/P16)

  • Robert Tampé

Deutsche Forschungsgemeinschaft (CRC 807/24)

  • Nina Morgner

European Research Council (798121)

  • Robert Tampé

JSPS Grants-in-Aid for Research Fellowship (P15333)

  • Richard Obexer

Japan Society for the Promotion of Science (JP20H05618)

  • Hiroaki Suga

Japan Society for the Promotion of Science (JP20am0101090)

  • Hiroaki Suga

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. David Drew, Stockholm University, Sweden

Version history

  1. Received: February 21, 2021
  2. Accepted: April 29, 2021
  3. Accepted Manuscript published: April 30, 2021 (version 1)
  4. Version of Record published: May 12, 2021 (version 2)

Copyright

© 2021, Stefan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Erich Stefan
  2. Richard Obexer
  3. Susanne Hofmann
  4. Khanh Vu Huu
  5. Yichao Huang
  6. Nina Morgner
  7. Hiroaki Suga
  8. Robert Tampé
(2021)
De-novo macrocyclic peptides dissect energy coupling of a heterodimeric ABC transporter by multimode allosteric inhibition
eLife 10:e67732.
https://doi.org/10.7554/eLife.67732

Share this article

https://doi.org/10.7554/eLife.67732

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