An Improved Mechanism‐Based Cross‐Linker for Multiplexed Kinase Detection and Inhibition in a Complex Proteome

Liu, Kai; Kalesh, Karunakaran A.; Ong, L. B.; Yao, Shao Q.

doi:10.1002/cbic.200800212

Cited by 15 publications

(20 citation statements)

References 24 publications

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“…This analog is predicted to serve as a less reactive substitute to o -phthaldialdehyde, since it contains a sterically hindered and less electron deficient acetyl group, while still reacting with thiols and amines to produce isoindoles 31. Naphtalene-2,3-dialdehyde 12 was also included in the screen since Yao and coworkers reported an improved version of cross-linker 1 , containing naphthalene-2,3-dialdehyde 12. Replacement of the acetyl group in o -acetylbenzaldehyde 11 with a cyanogroup led to o -cyanobenzaldehyde 13 as another possible candidate with reduced reactivity, this cyanoaldehyde forms a thiazolidine based product rather than isoindole 32.…”

Section: Resultsmentioning

confidence: 99%

“…Yao and coworkers recently reported a modified version of cross-linker 1 that is based on 2,3-naphthalenedicarboxaldehyde rather than on o -phthaldialdehyde. This substitution improves the efficiency of the cross-linking reaction in cell lysates 12. In this report, we systematically explore two of the structural elements that diminish the utility of cross-linker 1 in cell lysates and describe a new series of cross-linkers with greatly enhanced selectivity for the desired kinase substrate cross-linking reaction.…”

Section: Introductionmentioning

confidence: 99%

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Tuning a Three-Component Reaction For Trapping Kinase Substrate Complexes

et al. 2008

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The upstream protein kinases responsible for thousands of phosphorylation events in the phosphoproteome remain to be discovered. We developed a three-component chemical reaction which converts the transient non-covalent substrate-kinase complex into a covalently cross-linked product by utilizing a dialdehyde based cross-linker, 1. Unfortunately the reaction of 1 with a lysine in the kinase active site and an engineered cysteine on the substrate to form an isoindole cross-linked product could not be performed in the presence of competing cellular proteinsdue to non-specific side reactions. In order to more selectively target the cross-linker to protein kinases in cell lysates we replaced the weak, kinase-binding adenosine moiety of 1 with a potent protein kinase inhibitor scaffold. In addition, we replaced the o-phthaldialdehyde moiety in 1 with a less reactive thiophene-2,3-dicarboxaldehyde moiety. The combination of these two structural modifications provides for cross-linking of a cysteine containing substrate to its corresponding kinase in the presence of competing cellular proteins.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tuning a Three-Component Reaction For Trapping Kinase Substrate Complexes

et al. 2008

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“…Subsequent improvements were made by replacement of the OPA group with naphthalene-2,3-dialdehyde (NDA) and thiophene-2,3-dicarboxaldehyde, giving 27 and 28, respectively. [39,40] The improved probes were able to cross-link kinase/pseudo-substrate complexes more efficiently in cell lysates. In an alternative approach that obviates the use of pseudo-substrates, Suwal and Pflum designed cross-linker (29), an ATP analogue with its g-phosphate conjugated to a photo-crosslinker.…”

Section: Abps For Protein Phosphatases and Kinasesmentioning

confidence: 99%

Current Chemical Biology Tools for Studying Protein Phosphorylation and Dephosphorylation

Tan

et al. 2011

Chemistry A European J

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Amongst different posttranslational events involved in cellular-signaling pathways, phosphorylation and dephosphorylation of proteins are the most prevalent. Aberrant regulations in the cellular phosphoproteome network are implicated in most major human diseases. Consequently, kinases and phosphatases are two of the most important groups of drug targets in medicinal research today. A major challenge in the understanding of protein phosphorylation and dephosphorylation is the sheer complexity of the phosphoproteome network and the lack of tools capable of studying protein phosphorylation and dephosphorylation as they occur in cells. We highlight herein various chemical biology tools that have emerged in the last decade for such studies. First, we discuss the use of small-molecule mimics of phosphoamino acids and their use in elucidating the function of protein phosphorylation and dephosphorylation. We also introduce recent advances in the field of activity-based protein profiling (ABPP) for proteome-wide detection of protein phosphorylation and dephosphorylation. We next discuss the key concepts in the design of peptide- and protein-based biosensors capable of real-time reporting of phosphorylation/dephosphorylation events. Finally, we highlight the application of peptide and small-molecule microarrays (SMMs), and their applications in high-throughput screening and discovery of new compounds related to phosphorylation/dephosphorylation.

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“…Clearly, steric and electronic effects are important factors in this cross-linking reaction and govern its specificity. However, the use of naphthalene-2,3-dicarboxaldehyde adenosine (Guest 2) (Figure 5) instead of o-phthaldialdehydebenzoyl adenosine (Guest 1) for cross-linking endogenous kinases in mammalian cells was demonstrated with high specificity and selectivity 37. Because of its chemical properties, the Guest 2 is a better structural fit in the kinase active site than Guest 1.…”

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confidence: 98%

Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions

Martić

Kraatz

2013

Chem. Sci.

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EDGE ARTICLEAndrew J. deMello, Joshua B. Edel et al. Rapid cell extraction in aqueous twophase microdroplet systems PERSPECTIVE Barry M. Trost et al. Catalytic asymmetric allylic alkylation employing heteroatom nucleophiles: a powerful method for C-X bond formation Abstract Current interests in biochemical transformations based on protein kinase-catalyzed phosphorylations drive the identification and characterization of biological targets and potential inhibitors of protein kinase activity. A simple transfer of a phosphate group from adenosine triphosphate (ATP) to the Ser/Thr/Tyr residues of target proteins drives cellular processes, including cell expression, growth, and death. Currently, three major experimental approaches towards kinome analysis are available a) genetic engineering of protein kinases, b) modifications of target substrates, and c) derivatization of ATP co-substrate. Each approach offers advantages but also has disadvantages, which are discussed in this perspective, alongside with a rationale for designing and developing biological tools for kinome study.

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An Improved Mechanism‐Based Cross‐Linker for Multiplexed Kinase Detection and Inhibition in a Complex Proteome

Cited by 15 publications

References 24 publications

Tuning a Three-Component Reaction For Trapping Kinase Substrate Complexes

Tuning a Three-Component Reaction For Trapping Kinase Substrate Complexes

Current Chemical Biology Tools for Studying Protein Phosphorylation and Dephosphorylation

Chemical biology toolkit for exploring protein kinase catalyzed phosphorylation reactions

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