@article {285,
	title = {Ligand interaction landscape of transcription factors and essential enzymes in E.~coli.},
	journal = {Cell},
	year = {2025},
	month = {2025 Jan 22},
	abstract = {<p>Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing of biochemical processes, but the discovery of endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision mass spectrometry and high-resolution molecular docking to precisely map the physical associations of 296 chemically diverse small-molecule metabolite ligands with 69 distinct essential enzymes and 45 transcription factors in the gram-negative bacterium Escherichia coli. We then conducted systematic metabolic pathway integration, pan-microbial evolutionary projections, and independent in-depth biophysical characterization experiments to define the functional significance of ligand interfaces. This effort revealed principles governing functional crosstalk on a network level, divergent patterns of binding pocket conservation, and scaffolds for designing selective chemical probes. This structurally resolved ligand interactome mapping pipeline can be scaled to illuminate the native small-molecule networks of complete cells and potentially entire multi-cellular communities.</p>},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2025.01.003},
	author = {Peng, Hui and Kotelnikov, Sergei and Egbert, Megan E and Ofaim, Shany and Stevens, Grant C and Phanse, Sadhna and Saccon, Tatiana and Ignatov, Mikhail and Dutta, Shubham and Istace, Zoe and Moutaoufik, Mohamed Taha and Aoki, Hiroyuki and Kewalramani, Neal and Sun, Jianxian and Gong, Yufeng and Padhorny, Dzmitry and Poda, Gennady and Alekseenko, Andrey and Porter, Kathryn A and Jones, George and Rodionova, Irina and Guo, Hongbo and Pogoutse, Oxana and Datta, Suprama and Saier, Milton and Crovella, Mark and Vajda, Sandor and Moreno-Hagelsieb, Gabriel and Parkinson, John and Segre, Daniel and Babu, Mohan and Kozakov, Dima and Emili, Andrew}
}
@article {97,
	title = {An Unbiased Chemical Proteomics Method Identifies FabI as the Primary Target of 6-OH-BDE-47.},
	journal = {Environ Sci Technol},
	volume = {50},
	year = {2016},
	month = {2016 Oct 18},
	pages = {11329-11336},
	abstract = {<p>Determination of the physical interactions of environmental chemicals with cellular proteins is important for characterizing biological and toxic mechanism of action. Yet despite the discovery of numerous bioactive natural brominated compounds, such as hydroxylated polybrominated diphenyl ethers (OH-PBDEs), their corresponding protein targets remain largely unclear. Here, we reported a systematic and unbiased chemical proteomics assay (Target Identification by Ligand Stabilization, TILS) for target identification of bioactive molecules based on monitoring ligand-induced thermal stabilization. We first validated the broad applicability of this approach by identifying both known and unexpected proteins bound by diverse compounds (anticancer drugs, antibiotics). We then applied TILS to identify the bacterial target of 6-OH-BDE-47 as enoyl-acyl carrier protein reductase (FabI), an essential and widely conserved enzyme. Using affinity pull-down and in vitro enzymatic assays, we confirmed the potent antibacterial activity of 6-OH-BDE-47 occurs via direct binding and inhibition of FabI. Conversely, overexpression of FabI rescued the growth inhibition of Escherichia coli by 6-OH-BDE-47, validating it as the primary in vivo target. This study documents a chemical proteomics strategy for identifying the physical and functional targets of small molecules, and its potential high-throughput application to investigate the modes-of-action of environmental compounds.</p>},
	issn = {1520-5851},
	doi = {10.1021/acs.est.6b03541},
	author = {Peng, Hui and Guo, Hongbo and Pogoutse, Oxana and Wan, Cuihong and Hu, Lucas Z and Ni, Zuyao and Emili, Andrew}
}
