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Cell-based proteome profiling using an affinity-based probe (AfBP) derived from 3-deazaneplanocin A (DzNep).

Eric K W Tam¹, Zhengqiu Li, Yi Ling Goh

¹Institute of Chemical and Engineering Sciences, 8 Biomedical Grove, Neuros #07-01, 138665, Singapore.

Chemistry, an Asian Journal

|June 11, 2013

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Researchers developed a new chemical probe, DZ-1, derived from 3-Deazaneplanocin A (DzNep), a histone methylation inhibitor. This probe helps identify potential cellular targets of DzNep in live cells, advancing epigenetic research and cancer therapy development.

Area of Science:

Epigenetics
Chemical Biology
Proteomics

Background:

3-Deazaneplanocin A (DzNep) is a histone methylation inhibitor with therapeutic potential.
Its precise molecular mechanisms and cellular targets remain largely unknown.
Understanding DzNep's interactions is crucial for its application in epigenetic research and cancer therapy.

Purpose of the Study:

To design and synthesize novel small-molecule probes derived from DzNep.
To identify potential cellular targets of DzNep in live mammalian cells using these probes.
To investigate the cellular activity and target engagement of DzNep.

Main Methods:

Design and synthesis of a 'clickable' affinity-based probe (DZ-1) from DzNep.
Synthesis of control probes to minimize false positives.

Keywords:

affinity-based probes click chemistry epigenetics inhibitors proteomics

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In-situ proteome profiling in live mammalian cells.

Affinity pull-down assays followed by LC-MS/MS analysis.

Main Results:

DZ-1 demonstrated high cell permeability and anti-apoptotic activity similar to DzNep.
Proteome profiling identified previously unreported proteins interacting with DzNep.
These novel protein interactions may represent unknown cellular off-targets of DzNep.

Conclusions:

The developed probe (DZ-1) is effective for identifying DzNep targets in native cellular environments.
The study reveals potential novel off-targets of DzNep, expanding our understanding of its biological activity.
Findings support DzNep's utility as a chemical probe in epigenetics and as a potential cancer therapeutic agent.