1. Cancer Biology
  2. Structural Biology and Molecular Biophysics

Dynamics of human protein kinase Aurora A linked to drug selectivity

  1. Warintra Pitsawong
  2. Vanessa Buosi
  3. Renee Otten
  4. Roman V Agafonov
  5. Adelajda Zorba
  6. Nadja Kern
  7. Steffen Kutter
  8. Gunther Kern
  9. Ricardo AP Pádua
  10. Xavier Meniche
  11. Dorothee Kern  Is a corresponding author
  1. Howard Hughes Medical Institute, Brandeis University, United States
  2. University of Massachusetts Medical School, United States
https://doi.org/10.7554/eLife.36656
Share this article
Cite this article
  1. Warintra Pitsawong
  2. Vanessa Buosi
  3. Renee Otten
  4. Roman V Agafonov
  5. Adelajda Zorba
  6. Nadja Kern
  7. Steffen Kutter
  8. Gunther Kern
  9. Ricardo AP Pádua
  10. Xavier Meniche
  11. Dorothee Kern
(2018)
Dynamics of human protein kinase Aurora A linked to drug selectivity
eLife 7:e36656.
https://doi.org/10.7554/eLife.36656
  2. Download BibTeX
  3. Download .RIS

Abstract

Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinases Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Aurora A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome.

Data availability

Diffraction data have been deposited in PDB under the accession codes 6CPE, 6CPF, 6CPG.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Warintra Pitsawong

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5438-1783

  2. Vanessa Buosi

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Renee Otten

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7342-6131

  4. Roman V Agafonov

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Adelajda Zorba

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4452-8419

  6. Nadja Kern

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Steffen Kutter

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  8. Gunther Kern

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  9. Ricardo AP Pádua

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    Competing interests
    The authors declare that no competing interests exist.

  10. Xavier Meniche

    Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.

  11. Dorothee Kern

    Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
    For correspondence
    dkern@brandeis.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7631-8328

Funding

Howard Hughes Medical Institute

  • Dorothee Kern

National Institutes of Health (GM100966-01)

  • Dorothee Kern

U.S. Department of Energy (DE-FG02-05ER15699)

  • Dorothee Kern

Damon Runyon Cancer Research Foundation (DRG-2114-12)

  • Renee Otten

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

Copyright

© 2018, Pitsawong 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.

Metrics

  • 4,579
    views
  • 794
    downloads
  • 41
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Warintra Pitsawong
  2. Vanessa Buosi
  3. Renee Otten
  4. Roman V Agafonov
  5. Adelajda Zorba
  6. Nadja Kern
  7. Steffen Kutter
  8. Gunther Kern
  9. Ricardo AP Pádua
  10. Xavier Meniche
  11. Dorothee Kern
(2018)
Dynamics of human protein kinase Aurora A linked to drug selectivity
eLife 7:e36656.
https://doi.org/10.7554/eLife.36656

Share this article

https://doi.org/10.7554/eLife.36656

Categories and tags

Research organism

Further reading

    1. Cancer Biology
    2. Genetics and Genomics

    Recurrent disruption of tumour suppressor genes in cancer by somatic mutations in cleavage and polyadenylation signals

    Yaroslav Kainov, Fursham Hamid, Eugene V Makeyev
    Research Article

    The expression of eukaryotic genes relies on the precise 3'-terminal cleavage and polyadenylation of newly synthesized pre-mRNA transcripts. Defects in these processes have been associated with various diseases, including cancer. While cancer-focused sequencing studies have identified numerous driver mutations in protein-coding sequences, noncoding drivers – particularly those affecting the cis-elements required for pre-mRNA cleavage and polyadenylation – have received less attention. Here, we systematically analysed somatic mutations affecting 3'UTR polyadenylation signals in human cancers using the Pan-Cancer Analysis of Whole Genomes (PCAWG) dataset. We found a striking enrichment of cancer-specific somatic mutations that disrupt strong and evolutionarily conserved cleavage and polyadenylation signals within tumour suppressor genes. Further bioinformatics and experimental analyses conducted as a part of our study suggest that these mutations have a profound capacity to downregulate the expression of tumour suppressor genes. Thus, this work uncovers a novel class of noncoding somatic mutations with significant potential to drive cancer progression.

    1. Cancer Biology
    2. Immunology and Inflammation

    Tissue-resident natural killer cells support survival in pancreatic cancer through promotion of cDC1-CD8 T activity

    Simei Go, Constantinos Demetriou ... Eric O Neill
    Research Article

    The immunosuppressive microenvironment in pancreatic ductal adenocarcinoma (PDAC) prevents tumor control and strategies to restore anti-cancer immunity (i.e. by increasing CD8 T-cell activity) have had limited success. Here, we demonstrate how inducing localized physical damage using ionizing radiation (IR) unmasks the benefit of immunotherapy by increasing tissue-resident natural killer (trNK) cells that support CD8 T activity. Our data confirms that targeting mouse orthotopic PDAC tumors with IR together with CCR5 inhibition and PD1 blockade reduces E-cadherin positive tumor cells by recruiting a hypoactive NKG2D-ve NK population, phenotypically reminiscent of trNK cells, that supports CD8 T-cell involvement. We show an equivalent population in human single-cell RNA sequencing (scRNA-seq) PDAC cohorts that represents immunomodulatory trNK cells that could similarly support CD8 T-cell levels in a cDC1-dependent manner. Importantly, a trNK signature associates with survival in PDAC and other solid malignancies revealing a potential beneficial role for trNK in improving adaptive anti-tumor responses and supporting CCR5 inhibitor (CCR5i)/αPD1 and IR-induced damage as a novel therapeutic approach.

    1. Cancer Biology

    Increased inflammatory signature in myeloid cells of non-small cell lung cancer patients with high clonal hematopoiesis burden

    Hyungtai Sim, Hyun Jung Park ... Murim Choi
    Research Article

    Clonal hematopoiesis of indeterminate potential (CHIP) allows estimation of clonal dynamics and documentation of somatic mutations in the hematopoietic system. Recent studies utilizing large cohorts of the general population and patients have revealed significant associations of CHIP burden with age and disease status, including in cancer and chronic diseases. An increasing number of cancer patients are treated with immune checkpoint inhibitors (ICIs), but the association of ICI response in non-small cell lung cancer (NSCLC) patients with CHIP burden remains to be determined. We collected blood samples from 100 metastatic NSCLC patients before and after ICI for high-depth sequencing of the CHIP panel and 63 samples for blood single-cell RNA sequencing. Whole exome sequencing was performed in an independent replication cohort of 180 patients. The impact of CHIP status on the immunotherapy response was not significant. However, metastatic lung cancer patients showed higher CHIP prevalence (44/100 for patients vs. 5/42 for controls; p = 0.01). In addition, lung squamous cell carcinoma (LUSC) patients showed increased burden of larger clones compared to lung adenocarcinoma (LUAD) patients (8/43 for LUSC vs. 2/50 for LUAD; p = 0.04). Furthermore, single-cell RNA-seq analysis of the matched patients showed significant enrichment of inflammatory pathways mediated by NF-κB in myeloid clusters of the severe CHIP group. Our findings suggest minimal involvement of CHIP mutation and clonal dynamics during immunotherapy but a possible role of CHIP as an indicator of immunologic response in NSCLC patients.