Photoaffinity labeling of transcription factors by DNA-templated crosslinking

Liu, Ying; Zheng, Wenlu; Zhang, Wan; Chen, Nan; Liu, Yang; Chen, Li; Chen, Xingshuo; Zheng, Haifeng; Li, Xiaoyu

doi:10.1039/c4sc01953a

Cited by 36 publications

(31 citation statements)

References 92 publications

(114 reference statements)

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“…It is also worth noting that the approach used by Yao et al. was able to capture indirectly binding targets in the protein complex; a highly useful capability that has yet to be explored with the DPAL method (e.g., varying the site of CP hybridization on the BP DNA). Currently, we are studying other potential targets reported in Figure c to investigate their binding modes with MLN8237 (direct or indirect) and functional connections with the biological activities of MLN8237.…”

Section: Discussionmentioning

confidence: 99%

“…For example, the groups of Hosoya, Suzuki, and Young designed several types of highly compact “all‐in‐one” affinity probes for target ID; Yao and co‐workers developed a “minimalist” linker strategy to minimize the impact of add‐on structures on target binding; and the group of Cravatt designed a series of fully functionalized small‐molecule probes that incorporated the cross‐linker as part of the binding structure . Previously, we reported a DNA‐based affinity labeling method named DPAL . Instead of using a single trifunctional probe, DPAL has a dual‐probe system: a BP, in which the small molecule is conjugated with a short DNA strand, and a CP, in which the affinity tag and the cross‐linker are conjugated with a complementary DNA strand (Figure b).…”

Section: Introductionmentioning

confidence: 99%

“…Because CP is not involved in target binding, potential interference from the affinity tag and the cross‐linker are obviated. Previously, we reported the proof‐of‐principle target ID studies of DPAL for small molecules and nucleic acids . Herein, we report the application of DPAL in identifying the cellular targets of Alisertib, which is an aurora kinase A (AKA) inhibitor and an anticancer drug candidate being tested in clinical trials …”

Section: Introductionmentioning

confidence: 99%

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Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA‐Programmed Affinity Labeling

Wang

Cao

Chen

et al. 2017

Chemistry A European J

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Accurate identification of the molecular targets of bioactive small molecules is a highly important yet challenging task in biomedical research. Previously, a method named DPAL (DNA-programmed affinity labeling) for labeling and identifying the cellular targets of small molecules and nucleic acids was developed. Herein, DPAL is applied for the target identification of Alisertib (MLN8237), which is a highly specific aurora kinase A (AKA) inhibitor and a drug candidate being tested in clinical trials for cancer treatment. Apart from the well-established target of AKA, several potential new targets of MLN8237 were identified. Among them, p38 mitogen-activated protein kinase (p38) and laminin receptor (LAMR) were validated to be implicated in the anticancer activities of MLN8237. Interestingly, these new targets were not identified with non-DNA-based affinity probes. This work may facilitate an understanding of the molecular basis of the efficacy and side effects of MLN8237 as a clinical drug candidate. On the other hand, this work has also demonstrated that the method of DPAL could be a useful tool for target identification of bioactive small molecules.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA‐Programmed Affinity Labeling

Wang

Cao

Chen

et al. 2017

Chemistry A European J

Self Cite

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“…Furthermore, we confirmed that this salt effect also works with non-DNA-based probes and probes with benzophenone and phenylazide, two other commonly used photo-crosslinkers. We have been applying this salt effect when characterizing small molecule-protein and DNAprotein interactions (Li et al 2013a(Li et al , 2014bLiu et al 2015).…”

Section: The Salt Effectmentioning

confidence: 98%

“…Furthermore, we have developed the second generation of DPAL by utilizing the multivalency effect; ) a trivalent arylazide crosslinker has significantly improved the labeling yield of DPAL (Li et al 2014b). In addition, recently we extended the application of DPAL to study DNAbinding proteins, such as transcription factors and proteins recognizing epigenetic marks (Liu et al 2015).…”

Section: Dna-programmed Affinity Labeling (Dpal)mentioning

confidence: 99%

Affinity purification in target identification: the specificity challenge

Zheng

2015

Arch. Pharm. Res.

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Since phenotype-based screening directly evaluates capability of small molecules for modulating biology in actual biological systems, it has become an important discover modality in modern pharmaceutical sciences. However, in order to fully elucidate the molecular mechanism underlying the bioactivity of small molecules, identification of their biological targets is an indispensable step. Among the many target identification strategies developed during the past several decades, affinity purification remains to be one of the most important and powerful approaches, as it can directly reveal the physical interactions between small molecules and their biomolecular targets. However, due to the complexity of the proteome and the diversity of small molecule-protein interactions, affinity purification faces the specificity challenge: how to identify the true specific targets from the non-specific background? Focusing on this challenge, in this review, we briefly introduce the history and background of affinity purification, and then we discussed the major technological developments aiming to address this challenge. We have summarized these approaches in two categories: noise reduction and comparative distinction. This review also highlights the importance of choosing an integrated approach combining multiple methods to achieving success in target identification.

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Development of a DNA‐Templated Peptide Probe for Photoaffinity Labeling and Enrichment of the Histone Modification Reader Proteins

Bai

Jin

et al. 2016

Angewandte Chemie

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Histone post-translational modifications (HPTMs) provide signal platforms to recruit proteins or protein complexes to regulate gene expression. Therefore, the identification of these recruited partners (readers) is essential to understand the underlying regulatory mechanisms. However, it is still a major challenge to profile these partners because their interactions with HPTMs are rather weak and highly dynamic. Herein we report the development of a HPTM dual probe based on DNA-templated technology and a photo-crosslinking method for the identification of HPTM readers. By using the trimethylation of histone H3 lysine 4, we demonstrated that this HPTM dual probe can be successfully utilized for labeling and enrichment of HPTM readers, as well as for the discovery of potential HPTM partners. This study describes the development of a new chemical proteomics tool for profiling HPTM readers and can be adapted for broad biomedical applications.

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Photoaffinity labeling of transcription factors by DNA-templated crosslinking

Abstract: A dual-probe system can specifically capture DNA-binding proteins with an unmodified binding site.

Cited by 36 publications

References 92 publications

Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA‐Programmed Affinity Labeling

Target Identification of Kinase Inhibitor Alisertib (MLN8237) by Using DNA‐Programmed Affinity Labeling

Affinity purification in target identification: the specificity challenge

Development of a DNA‐Templated Peptide Probe for Photoaffinity Labeling and Enrichment of the Histone Modification Reader Proteins

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