Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2

Benedict Tilman Berger, Marta Amaral, Daria B. Kokh, Ariane Nunes-Alves, Djordje Musil, Timo Heinrich, Martin Schröder, Rebecca Neil, Jing Wang, Iva Navratilova, Joerg Bomke, Jonathan M. Elkins, Susanne Müller, Matthias Frech, Rebecca C. Wade, Stefan Knapp (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

Abstract

There is increasing evidence of a significant correlation between prolonged drug-target residence time and increased drug efficacy. Here, we report a structural rationale for kinetic selectivity between two closely related kinases: focal adhesion kinase (FAK) and proline-rich tyrosine kinase 2 (PYK2). We found that slowly dissociating FAK inhibitors induce helical structure at the DFG motif of FAK but not PYK2. Binding kinetic data, high-resolution structures and mutagenesis data support the role of hydrophobic interactions of inhibitors with the DFG-helical region, providing a structural rationale for slow dissociation rates from FAK and kinetic selectivity over PYK2. Our experimental data correlate well with computed relative residence times from molecular simulations, supporting a feasible strategy for rationally optimizing ligand residence times. We suggest that the interplay between the protein structural mobility and ligand-induced effects is a key regulator of the kinetic selectivity of inhibitors of FAK versus PYK2. Berger et al. present a rationale for the selectivity of PF-562271 on FAK over PYK2. Investigation of an inhibitor series by structural and biophysical, computational, as well as cellular techniques provided a structure-kinetic-relationship and revealed a ligand-induced helical DFG motif resulting in kinetic selectivity of FAK inhibitors over PYK2.

Original languageEnglish
Number of pages20
JournalCell Chemical Biology
Early online date25 Jan 2021
DOIs
Publication statusE-pub ahead of print - 25 Jan 2021

Keywords

  • focal adhesion kinase (FAK)
  • kinase inhibitor
  • ligand residence time
  • NanoBRET
  • proline-rich tyrosine kinase 2 (PYK2)
  • structure-kinetic-relationship
  • τRAMD

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