Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

Zhang, Meng Yao; Yang, Hoon Shik; Ortiz, Gloria; Trnka, Michael J.; Petronikolou, Nektaria; Burlingame, Alma L.; DeGrado, William F.; Fujimori, Danica Galonić

doi:10.1039/d2sc00555g

Cited by 17 publications

(12 citation statements)

References 56 publications

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“…Notably, the targeting strategy can be expected to be transferable to other Gram-negative bacteria due to the high conservation of the FtsQB complex. Finally, the presented approach is an uncommon example of a peptide-based covalent inhibitor targeting a non-catalytic amino acid. − This highlights the potential of proteomimetic molecules with a covalent mode-of-action as inhibitors of challenging protein–protein interactions.…”

Section: Discussionmentioning

confidence: 97%

Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex

et al. 2022

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The use of antibiotics is threatened by the emergence and spread of multidrug-resistant strains of bacteria. Thus, there is a need to develop antibiotics that address new targets. In this respect, the bacterial divisome, a multi-protein complex central to cell division, represents a potentially attractive target. Of particular interest is the FtsQB subcomplex that plays a decisive role in divisome assembly and peptidoglycan biogenesis in E. coli . Here, we report the structure-based design of a macrocyclic covalent inhibitor derived from a periplasmic region of FtsB that mediates its binding to FtsQ. The bioactive conformation of this motif was stabilized by a customized cross-link resulting in a tertiary structure mimetic with increased affinity for FtsQ. To increase activity, a covalent handle was incorporated, providing an inhibitor that impedes the interaction between FtsQ and FtsB irreversibly. The covalent inhibitor reduced the growth of an outer membrane-permeable E. coli strain, concurrent with the expected loss of FtsB localization, and also affected the infection of zebrafish larvae by a clinical E. coli strain. This first-in-class inhibitor of a divisome protein–protein interaction highlights the potential of proteomimetic molecules as inhibitors of challenging targets. In particular, the covalent mode-of-action can serve as an inspiration for future antibiotics that target protein–protein interactions.

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Section: Discussionmentioning

confidence: 97%

Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex

et al. 2022

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“…[18] These findings were surprising given that OSF has been shown to react with lysine residues when targeted with a ligand directing group. [21,25] This general lack of lysine modification by our simple OSF fragment probe may be due to the relative small size of the fragment and limited labeling time (2 hours).…”

Section: Resultsmentioning

confidence: 99%

Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows

Faucher

Abegg²,

Ipock

et al. 2023

Preprint

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Macrocyclic peptides are attractive for chemoproteomic applications due to their modular synthesis and potential for high target selectivity. We describe a solid phase synthesis method for the efficient generation of libraries of small macrocycles that contain an electrophile and alkyne handle. The modular synthesis produces libraries that can be directly screened using simple SDS-PAGE readouts and then optimal lead molecules applied to proteomic analysis. We generated a library of 480 macrocyclic peptides containing the weakly reactive fluorosulfate (OSF) electrophile. Initial screening of a subset of the library containing each of the various diversity elements identified initial molecules of interest. The corresponding positional and confirmational isomers were then screened to select molecules that showed specific protein labeling patterns that were dependent on the probe structure. The most promising hits were applied to standard chemoproteomic workflows to identify protein targets. Our results demonstrate the feasibility of rapid, on-resin synthesis of diverse macrocyclic electrophiles to generate new classes of covalent ligands.

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“…A unique strategy to design peptidomimetic antagonists for the KDM5A PHD3 has been developed by Zhang et al. ( 59 ). These macrocyclic peptides mimic methylated H3K4 but have K4me2 and T6 covalently linked by lactam, thioether, or triazole linkers ( Fig.…”

Section: Strategies To Inhibit Phd Fingersmentioning

confidence: 99%

“…5 C ). Furthermore, some H3K4me3 mimetics bearing arylsulfonyl fluoride and arylfluorosulfate covalent warheads at Q5 can pull down exogenously expressed KDM5A PHD3 from the lysate of HEK293T cells ( 59 ). Alternatively, the H3K4me3–PHD complex formation can be blocked by supramolecular caging compounds and chelating macrocycles, such as calixarenes ( 60 ).…”

Section: Strategies To Inhibit Phd Fingersmentioning

confidence: 99%