Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism

Ning Ma, Lisa G. Lippert, Titu Devamani, Benjamin Levy, Sangbae Lee, Manbir Sandhu, Nagarajan Vaidehi, Sivaraj Sivaramakrishnan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.

Original languageEnglish (US)
Pages (from-to)6387-6390
Number of pages4
JournalBiochemistry
Volume57
Issue number45
DOIs
StatePublished - Nov 13 2018

Bibliographical note

Funding Information:
This research was funded in part by the National Institute of Health (NIH) Director’s New Innovator Award (1DP2 CA186752-01) and NIH MIRA award (1R35GM126940-01) to S.S. The work performed in N.V.’s laboratory was funded by NIH Grant R01GM097261. Notes The authors declare no competing financial interest.

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