7FIC

Reversible lysine-targeted probes reveal residence time-based kinase selectivity in vivo

Summary for 7FIC

• Entry DOI: 10.2210/pdb7fic/pdb
• Descriptor: Aurora kinase A, 6-[(5-cyclopropyl-1~{H}-pyrazol-3-yl)amino]-2-[4-[(3-methyl-4-oxidanyl-phenyl)methyl]piperazin-1-yl]-~{N}-prop-2-ynyl-pyrimidine-4-carboxamide, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: reversible lysine-targeted inhibitors; kinase, cell cycle
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 31311.18

Authors

Craven, G.B.,Wan, X.B.,Taunton, J. (deposition date: 2021-07-31, release date: 2022-06-08, Last modification date: 2024-10-09)

Primary citation

Yang, T.,Cuesta, A.,Wan, X.,Craven, G.B.,Hirakawa, B.,Khamphavong, P.,May, J.R.,Kath, J.C.,Lapek Jr., J.D.,Niessen, S.,Burlingame, A.L.,Carelli, J.D.,Taunton, J.
Reversible lysine-targeted probes reveal residence time-based kinase selectivity.
Nat.Chem.Biol., 18:934-941, 2022

PubMed Abstract: The expansion of the target landscape of covalent inhibitors requires the engagement of nucleophiles beyond cysteine. Although the conserved catalytic lysine in protein kinases is an attractive candidate for a covalent approach, selectivity remains an obvious challenge. Moreover, few covalent inhibitors have been shown to engage the kinase catalytic lysine in animals. We hypothesized that reversible, lysine-targeted inhibitors could provide sustained kinase engagement in vivo, with selectivity driven in part by differences in residence time. By strategically linking benzaldehydes to a promiscuous kinase binding scaffold, we developed chemoproteomic probes that reversibly and covalently engage >200 protein kinases in cells and mice. Probe-kinase residence time was dramatically enhanced by a hydroxyl group ortho to the aldehyde. Remarkably, only a few kinases, including Aurora A, showed sustained, quasi-irreversible occupancy in vivo, the structural basis for which was revealed by X-ray crystallography. We anticipate broad application of salicylaldehyde-based probes to proteins that lack a druggable cysteine.

PubMed: 35590003
DOI: 10.1038/s41589-022-01019-1

Experimental method

X-RAY DIFFRACTION (2.32 Å)