Cell‐Based Proteome Profiling Using an Affinity‐Based Probe (AfBP) Derived from 3‐Deazaneplanocin A (DzNep). Issue 8 (7th June 2013)

• Record Type: Journal Article
• Authors: Tam, Eric K. W.; Li, Zhengqiu; Goh, Yi Ling; Cheng, Xiamin; Wong, Sze Yue; Santhanakrishnan, Sridhar; Chai, Christina L. L.; Yao, Shao Q.
• Is Part Of: Chemistry, an Asian journal. Volume 8:Issue 8(2013:Aug.)
• Page Start: 1818
• Page End: 1828
• Publication Date: 2013-06-07
• Subjects: Chemistry -- Periodicals; 540.5
• DOI: 10.1002/asia.201300303
• Languages: English
• ISSNs: 1861-4728

Abstract

<abstract abstract-type="main" xml:lang="en"> <title>Abstract</title> <p>3‐Deazaneplanocin A (<bold>DzNep</bold>), a global histone <named-content id="d274e1082" content-type="reactionType" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">methylation</named-content> inhibitor, has attracted significant interest in epigenetic research in recent years. The molecular mechanism of action and the cellular off‐targets of <bold>DzNep</bold>, however, are still not well‐understood. Our aim was to develop novel <bold>DzNep</bold>‐derived small‐molecule probes suitable to be used in live mammalian cells for identification of potential cellular targets of <bold>DzNep</bold> under physiologically relevant settings. In the current study, we have successfully designed, synthesized, and tested one such probe, called <bold>Dz-1</bold>. <bold>Dz-1</bold> is a 'clickable' affinity‐based probe (A<italic>f</italic>BP) derived from <bold>DzNep</bold> with minimal structural modifications. The probe was found to be highly cell‐permeable, and possessed similar anti‐apoptotic activities as <bold>DzNep</bold> in MCF‐7 mammalian cells. Two additional control probes were made as negative labeling/pull‐down probes in order to minimize false identification of background proteins due to unavoidable, intrinsic nonspecific photo‐crosslinking reactions. All three probes were subsequently used for in‐situ proteome profiling in live mammalian cells, followed by large‐scale pull‐down/LC‐MS/MS analysis for identification of potential <named-content id="d274e1103" content-type="chemicalTechnology" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">cellular protein</named-content> targets that might interact with <bold>DzNep</bold> in native cellular environments. Our LC‐MS/MS results revealed some highly enriched proteins that had not been reported as potential <bold>DzNep</bold> targets. These proteins might constitute unknown cellular off‐targets of <bold>DzNep</bold>. Though further validation experiments are needed in order to unequivocally confirm these off‐targets, our findings shed new light on the future use of <bold>DzNep</bold> as a validated chemical probe for epigenetic research and as a potential drug candidate for <named-content id="d274e1115" content-type="chemicalTechnology" xlink:type="simple" xmlns:xlink="http://www.w3.org/1999/xlink">cancer therapy</named-content>.</p> </abstract>