High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design

  • Nat Commun. 2024 Mar 13;15(1):2265. doi: 10.1038/s41467-024-46375-9.
Victoria I Cushing  1 ,  Adrian F Koh  2 ,  Junjie Feng  1 ,  Kaste Jurgaityte  3 ,  Alexander Bondke  4 ,  Sebastian H B Kroll  4 ,  Marion Barbazanges  4  5 ,  Bodo Scheiper  4 ,  Ash K Bahl  6 ,  Anthony G M Barrett  4 ,  Simak Ali  7 ,  Abhay Kotecha  8 ,  Basil J Greber  9
Affiliations
  • 1. The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
  • 2. Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands.
  • 3. Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
  • 4. Department of Chemistry, Imperial College London, London, UK.
  • 5. Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, 4 Place Jussieu, 75252, Paris Cedex 05, France.
  • 6. Carrick Therapeutics, Nova UCD, Bellfield Innovation Park, Dublin 4, Ireland.
  • 7. Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK. [email protected].
  • 8. Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands. [email protected].
  • 9. The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK. [email protected].
PMID: 38480681 DOI: 10.1038/s41467-024-46375-9
Abstract

Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.

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