Structure-guided Inhibitor Design Expands the Scope of Analog-sensitive Kinase Technology

Overview

Journal ACS Chem Biol

Publisher American Chemical Society

Specialties Biochemistry
Biology

Date 2013 Jul 12

PMID 23841803

Citations 32

Authors

Chao Zhang

Michael S Lopez

Arvin C Dar

Eva LaDow

Steven Finkbeiner

Cai-Hong Yun

Michael J Eck

Kevan M Shokat

Affiliations

Soon will be listed here.

Abstract

Engineered analog-sensitive (AS) protein kinases have emerged as powerful tools for dissecting phospho-signaling pathways, for elucidating the cellular function of individual kinases, and for deciphering unanticipated effects of clinical therapeutics. A crucial and necessary feature of this technology is a bioorthogonal small molecule that is innocuous toward native cellular systems but potently inhibits the engineered kinase. In order to generalize this method, we sought a molecule capable of targeting divergent AS-kinases. Here we employ X-ray crystallography and medicinal chemistry to unravel the mechanism of current inhibitors and use these insights to design the most potent, selective, and general AS-kinase inhibitors reported to date. We use large-scale kinase inhibitor profiling to characterize the selectivity of these molecules as well as examine the consequences of potential off-target effects in chemical genetic experiments. The molecules reported here will serve as powerful tools in efforts to extend AS-kinase technology to the entire kinome and the principles discovered may help in the design of other engineered enzyme/ligand pairs.

Citing Articles

MAPK Cascades in Plant Microbiota Structure and Functioning.

Van Gerrewey T, Chung H J Microbiol. 2024; 62(3):231-248.

PMID: 38587594 DOI: 10.1007/s12275-024-00114-3.

Eph receptors and ephrins in cancer progression.

Pasquale E Nat Rev Cancer. 2023; 24(1):5-27.

PMID: 37996538 PMC: 11015936. DOI: 10.1038/s41568-023-00634-x.

Strategy toward Kinase-Selective Drug Discovery.

Zhang M, Liu Y, Jang H, Nussinov R J Chem Theory Comput. 2023; 19(5):1615-1628.

PMID: 36815703 PMC: 10018734. DOI: 10.1021/acs.jctc.2c01171.

CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation.

Tellier M, Zaborowska J, Neve J, Nojima T, Hester S, Fournier M EMBO Rep. 2022; 23(10):e54520.

PMID: 35980303 PMC: 9535751. DOI: 10.15252/embr.202154520.

Reactivity-based chemical-genetic study of protein kinases.

Miranda R, Zhang C RSC Med Chem. 2022; 13(7):783-797.

PMID: 35923719 PMC: 9298188. DOI: 10.1039/d1md00389e.

References

McGovern S, Helfand B, Feng B, Shoichet B . A specific mechanism of nonspecific inhibition. J Med Chem. 2003; 46(20):4265-72. DOI: 10.1021/jm030266r. View

Lampson M, Kapoor T . Unraveling cell division mechanisms with small-molecule inhibitors. Nat Chem Biol. 2006; 2(1):19-27. DOI: 10.1038/nchembio757. View

Garske A, Peters U, Cortesi A, Perez J, Shokat K . Chemical genetic strategy for targeting protein kinases based on covalent complementarity. Proc Natl Acad Sci U S A. 2011; 108(37):15046-52. PMC: 3174669. DOI: 10.1073/pnas.1111239108. View

Knight Z, Shokat K . Features of selective kinase inhibitors. Chem Biol. 2005; 12(6):621-37. DOI: 10.1016/j.chembiol.2005.04.011. View

Bain J, Plater L, Elliott M, Shpiro N, Hastie C, McLauchlan H . The selectivity of protein kinase inhibitors: a further update. Biochem J. 2007; 408(3):297-315. PMC: 2267365. DOI: 10.1042/BJ20070797. View

Liu Y, Bishop A, Witucki L, Kraybill B, Shimizu E, Tsien J . Structural basis for selective inhibition of Src family kinases by PP1. Chem Biol. 1999; 6(9):671-8. DOI: 10.1016/s1074-5521(99)80118-5. View

Schindler T, Sicheri F, Pico A, Gazit A, Levitzki A, Kuriyan J . Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. Mol Cell. 1999; 3(5):639-48. DOI: 10.1016/s1097-2765(00)80357-3. View

Hanke J, Gardner J, Dow R, Changelian P, Brissette W, Weringer E . Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. Study of Lck- and FynT-dependent T cell activation. J Biol Chem. 1996; 271(2):695-701. DOI: 10.1074/jbc.271.2.695. View

Savitt J, Singh D, Zhang C, Chen L, Folmer J, Shokat K . The in vivo response of stem and other undifferentiated spermatogonia to the reversible inhibition of glial cell line-derived neurotrophic factor signaling in the adult. Stem Cells. 2012; 30(4):732-40. PMC: 3894909. DOI: 10.1002/stem.1028. View

10.

Okuzumi T, Fiedler D, Zhang C, Gray D, Aizenstein B, Hoffman R . Inhibitor hijacking of Akt activation. Nat Chem Biol. 2009; 5(7):484-93. PMC: 2783590. DOI: 10.1038/nchembio.183. View

11.

Okuzumi T, Ducker G, Zhang C, Aizenstein B, Hoffman R, Shokat K . Synthesis and evaluation of indazole based analog sensitive Akt inhibitors. Mol Biosyst. 2010; 6(8):1389-402. PMC: 2932704. DOI: 10.1039/c003917a. View

12.

Zhang C, Kenski D, Paulson J, Bonshtien A, Sessa G, Cross J . A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases. Nat Methods. 2005; 2(6):435-41. DOI: 10.1038/nmeth764. View

13.

Manning G, Whyte D, Martinez R, Hunter T, Sudarsanam S . The protein kinase complement of the human genome. Science. 2002; 298(5600):1912-34. DOI: 10.1126/science.1075762. View

14.

Cipak L, Zhang C, Kovacikova I, Rumpf C, Miadokova E, Shokat K . Generation of a set of conditional analog-sensitive alleles of essential protein kinases in the fission yeast Schizosaccharomyces pombe. Cell Cycle. 2011; 10(20):3527-32. PMC: 3266181. DOI: 10.4161/cc.10.20.17792. View

15.

Liu Y, Warfield L, Zhang C, Luo J, Allen J, Lang W . Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol. 2009; 29(17):4852-63. PMC: 2725703. DOI: 10.1128/MCB.00609-09. View

16.

Weiss E, Bishop A, Shokat K, Drubin D . Chemical genetic analysis of the budding-yeast p21-activated kinase Cla4p. Nat Cell Biol. 2000; 2(10):677-85. DOI: 10.1038/35036300. View

17.

Witucki L, Huang X, Shah K, Liu Y, Kyin S, Eck M . Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme. Chem Biol. 2002; 9(1):25-33. DOI: 10.1016/s1074-5521(02)00091-1. View

18.

Sanchez-Ruiloba L, Cabrera-Poch N, Rodriguez-Martinez M, Lopez-Menendez C, Jean-Mairet R, Higuero A . Protein kinase D intracellular localization and activity control kinase D-interacting substrate of 220-kDa traffic through a postsynaptic density-95/discs large/zonula occludens-1-binding motif. J Biol Chem. 2006; 281(27):18888-900. DOI: 10.1074/jbc.M603044200. View

19.

Bishop A, Ubersax J, Petsch D, Matheos D, Gray N, Blethrow J . A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature. 2000; 407(6802):395-401. DOI: 10.1038/35030148. View

20.

Au-Yeung B, Levin S, Zhang C, Hsu L, Cheng D, Killeen N . A genetically selective inhibitor demonstrates a function for the kinase Zap70 in regulatory T cells independent of its catalytic activity. Nat Immunol. 2010; 11(12):1085-92. PMC: 3711183. DOI: 10.1038/ni.1955. View