Structural insight into the stabilization of microtubules by taxanes

  1. Andrea E Prota  Is a corresponding author
  2. Daniel Lucena-Agell
  3. Yuntao Ma
  4. Juan Estevez-Gallego
  5. Shuo Li
  6. Katja Bargsten
  7. Fernando Josa-Prado
  8. Karl-Heinz Altmann
  9. Natacha Gaillard
  10. Shinji Kamimura
  11. Tobias Mühlethaler
  12. Federico Gago
  13. Maria A Oliva
  14. Michel O Steinmetz
  15. Wei-Shuo Fang  Is a corresponding author
  16. J Fernando Díaz  Is a corresponding author
  1. Paul Scherrer Institute, Switzerland
  2. CSIC-Centro de Investigaciones Biologicas, Spain
  3. Chinese Academy of Medical Sciences & Peking Union Medical College, China
  4. ETH Zurich, Switzerland
  5. Chuo University, Japan
  6. Univeristy of Alcalá, Spain

Abstract

Paclitaxel (Taxol®) is a taxane and a first-line chemotherapeutic drug that stabilizes microtubules. While the interaction of paclitaxel with microtubules is well described, the current lack of high-resolution structural information on a tubulin-taxane complex precludes a comprehensive description of the binding determinants that affect the drug's mechanism of action. Here, we solved the crystal structure of the core baccatin III moiety of paclitaxel lacking the C13 side chain in complex with tubulin at 1.9 Å resolution. Based on this information, we engineered two tailor-made taxanes with modified C13 side chains, solved their crystal structures in complex with tubulin, and analyzed their effects along with those of paclitaxel, docetaxel, and baccatin III on the microtubule lattice by X-ray fiber diffraction. We then compared high-resolution structures of ligand-bound tubulin and microtubule complexes with apo forms and used molecular dynamics simulations to understand the consequences of taxane binding to tubulin as well as to simplified protofilament and microtubule-lattice models. Our combined approach sheds light on three mechanistic questions. Firstly, taxanes bind better to microtubules as compared to unassembled tubulin due to a dual structural mechanism: Tubulin assembly is linked to a conformational reorganization of the bM loop, which otherwise occludes ligand access to the taxane site, while the bulky C13 side chains preferentially recognize the microtubule-assembled over the unassembled conformational state of tubulin. Second, the occupancy of the taxane site by a ligand has no influence on the straightness of tubulin protofilaments. Finally, the longitudinal expansion of the microtubule lattices arises from the accommodation of the taxane core within the site, a process that is, however, not related to the microtubule stabilization mechanism of taxanes, as all analogs tested expand the microtubule lattice, despite the fact that one of them, Baccatin III, is biochemically inactive. In conclusion, our combined experimental and computational approach allowed us to describe the tubulin-taxane interaction in atomic detail and assess the structural determinants for binding.

Data availability

Diffraction data have been deposited in PDB under the accession codes 8BDE (T2R-TTL-BacIII), 8BDF (T2R-TTL-2a) and 8BDG ((T2R-TTL-2b).

The following data sets were generated

Article and author information

Author details

  1. Andrea E Prota

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
    For correspondence
    andrea.prota@psi.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0875-5339
  2. Daniel Lucena-Agell

    Structural and Chemical Biology, CSIC-Centro de Investigaciones Biologicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7314-8696
  3. Yuntao Ma

    Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Juan Estevez-Gallego

    Structural and Chemical Biology, CSIC-Centro de Investigaciones Biologicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
  5. Shuo Li

    Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Katja Bargsten

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Fernando Josa-Prado

    Structural and Chemical Biology, CSIC-Centro de Investigaciones Biologicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6162-3231
  8. Karl-Heinz Altmann

    Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  9. Natacha Gaillard

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  10. Shinji Kamimura

    Department of Biological Sciences, Chuo University, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  11. Tobias Mühlethaler

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  12. Federico Gago

    Department of Biomedical Sciences, Univeristy of Alcalá, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3071-4878
  13. Maria A Oliva

    Structural and Chemical Biology, CSIC-Centro de Investigaciones Biologicas, Madrid, Spain
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2215-4639
  14. Michel O Steinmetz

    Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  15. Wei-Shuo Fang

    Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
    For correspondence
    wfang@imm.ac.cn
    Competing interests
    The authors declare that no competing interests exist.
  16. J Fernando Díaz

    Structural and Chemical Biology, CSIC-Centro de Investigaciones Biologicas, Madrid, Spain
    For correspondence
    fer@cib.csic.es
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2743-3319

Funding

Ministerio de Ciencia e Innovación (PID2019-104545RB-I00)

  • J Fernando Díaz

Consejo Superior de Investigaciones Científicas (PIE 201920E111)

  • J Fernando Díaz

Fundación Tatiana Pérez de Guzmán el Bueno (Proyecto de Investigación en Neurociencia 2020)

  • J Fernando Díaz

European Union NextGenerationEU (H2020-MSCA-ITN-2019 860070 TUBINTRAIN)

  • Andrea E Prota
  • J Fernando Díaz

Swiss National Science Foundation (310030_192566)

  • Michel O Steinmetz

JSPS KAKENHI (16K07328/17H03668)

  • Shinji Kamimura

National Natural Science Foundation of China (30930108)

  • Wei-Shuo Fang

Chinese Academy of Medical Sciences (2016-I2M-1-010)

  • Wei-Shuo Fang

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

Reviewing Editor

  1. Kassandra M Ori-McKenney, University of California, United States

Version history

  1. Preprint posted: July 21, 2021 (view preprint)
  2. Received: November 11, 2022
  3. Accepted: March 3, 2023
  4. Accepted Manuscript published: March 6, 2023 (version 1)
  5. Version of Record published: March 28, 2023 (version 2)

Copyright

© 2023, Prota 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. Andrea E Prota
  2. Daniel Lucena-Agell
  3. Yuntao Ma
  4. Juan Estevez-Gallego
  5. Shuo Li
  6. Katja Bargsten
  7. Fernando Josa-Prado
  8. Karl-Heinz Altmann
  9. Natacha Gaillard
  10. Shinji Kamimura
  11. Tobias Mühlethaler
  12. Federico Gago
  13. Maria A Oliva
  14. Michel O Steinmetz
  15. Wei-Shuo Fang
  16. J Fernando Díaz
(2023)
Structural insight into the stabilization of microtubules by taxanes
eLife 12:e84791.
https://doi.org/10.7554/eLife.84791

Share this article

https://doi.org/10.7554/eLife.84791

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