An electroaffinity labelling platform for chemoproteomic-based target identification

Kawamata, Yu; Ryu, Keun Ah; Hermann, Gary N.; Sandahl, Alexander; Vantourout, Julien C.; Olow, Aleksandra; Adams, La-Tonya A.; Rivera‐Chao, Eva; Roberts, Lee R.; Gnaim, Samer; Nassir, Molhm; Oslund, Rob C.; Fadeyi, Olugbeminiyi O.; Baran, Phil S.

doi:10.1038/s41557-023-01240-y

Cited by 18 publications

(3 citation statements)

References 41 publications

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“…The challenges that we encountered obtaining high coverage for BCR and ABL1 align with prior chemoproteomic studies that sought to analyze BCR-ABL1-dasatinib interactions 30,89 and provides compelling evidence to support the need for new protein interaction mapping technologies that afford enhanced labeling efficiency to better capture low abundance protein targets using clinically relevant probe concentrations. The nascent photocatalytic labeling technologies, such as μMap 79,90,91 , together with electrochemical approaches 107 , latent electrophile approaches, such as the fluorosulfates used by inverse drug discovery 108 and ligand-directed (LD) chemistry 109,110 , are intriguing alternatives that may allow for target engagement studies using more clinically relevant drug and probe concentrations. The latter chemistries together with other non-light based platforms such as the recently reported BioTac approach 83 , are expected to be uniquely suited to in vivo applications.…”

Section: Discussionmentioning

confidence: 99%

Silyl Ether Enables High Coverage Chemoproteomic Interaction Site Mapping

Takechi,

Ngo,

Burton

et al. 2024

Preprint

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Most therapeutics are small molecules that function by interacting with specific protein targets. Consequently, delineating the protein targets, including the specific binding sites, for chemical probes and clinical candidates is essential to ensure potent on-target activity and to minimize engagement of unfavorable off-targets. The pairing of mass spectrometry-based chemoproteomics with photoaffinity labeling (PAL) has emerged as a favored approach to generate proteome-wide target engagement maps for reversible compounds. However, a key limitation of most PAL-based proteomic platforms is the absence of strategies that report precise binding sites and enable direct head-to-head comparisons of relative target engagement at these sites by different lead compounds. This gap stems from a confluence of factors including the complex fragmentation patterns for crosslinked peptides, poor recovery of peptides crosslinked with large hydrophobic molecules, and modification masses that differ between molecules of interest (MOI). To address these challenges, here we establish the Silyl Ether Enables Chemoproteomic Interaction and Target Engagement (SEE-CITE) approach. SEE-CITE incorporates an unprecedented fully functionalized chemically cleavable crosslinking handle that enables precise site-of-labeling identification and head-to-head comparisons of relative binding site engagement by chemically diverse compounds. To ensure high confidence localization of labeled residues, we also enabled enhanced mapping of photocrosslinked sites by extending the MSFragger algorithm of the FragPipe computational platform to report localization scores customized for PAL and SEE-CITE data. By benchmarking SEE-CITE using scout fragments and analogues of the FDA-approved kinase inhibitors dasatinib and asciminib, we identify known and novel binding sites, including for high impact targets, such as BCR-ABL1, STING, and COX5A.

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Section: Discussionmentioning

confidence: 99%

Silyl Ether Enables High Coverage Chemoproteomic Interaction Site Mapping

Takechi,

Ngo,

Burton

et al. 2024

Preprint

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“…However, the immobilization process often causes activity impairment of active molecules and solidphase carriers also bring significant steric hindrance to the active molecules, which will be unfavorable for binding targets and active molecules. Active probes have developed rapidly, have flexible functional designs, and have been successfully applied in target identification [34], cell imaging [35], and biomarker detection [36]. In the section on target identification, active probes usually require additional enrichment methods.…”

Section: Application Of Protacs In Target Identificationmentioning

confidence: 99%

Application of PROTACs in target identification and validation

Liu,

Liang,

Zhu

et al. 2024

Acta Materia Medica

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Proteolysis targeting chimeras (PROTACs), as a novel therapeutic drug model, has received widespread attention from academia and the pharmaceutical industry. PROTAC technology has led researchers to focus on developing chemical biology tool properties due to the unique operating mechanism and protein dynamic regulatory properties. In recent years the rapid development of PROTAC technology has gradually made PROTACs an essential tool for target identification and validation. To further promote the application of PROTAC tools in drug discovery and basic medical science research, this review distinguished target identification and validation concepts. Furthermore, research progress in PROTAC technology was summarized.

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“…Modification of these functional groups has improved on their utility in PAL experiments. Recent innovations have opened new directions for labeling experiments that rely on triggered probe activation in cells, including blue light-activated, [83] IRactivated, [128] or electrochemically-activated chemistries, [129] each of which enable new experimental conditions that avoid damaging UV light or allow experiments in tissue samples that are normally inaccessible with traditional PAL chemistries. In addition, the development of more high-efficiency chemistries that target specific amino acids, such as 2,5-tetrazoles, can enable activity-based protein profiling experiments that are traditionally only performed with covalent labeling chemistries.…”

Section: Future Directions Of Pal Chemistriesmentioning

confidence: 99%

Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions

West

Woo

2022

Israel Journal of Chemistry

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Photoaffinity labeling (PAL) is one of the few biochemical techniques that can give direct evidence of biomolecular interactions in cells. Several photoactivatable functional groups have been adapted for use in PAL since its first implementation. The diversity of these chemistries has expanded the scope and fidelity of PAL experiments, but also increased the considerations during PAL probe design. In this review, we describe the major chemistries used in PAL experiments and their relative benefits and disadvantages. We additionally discuss recent examples of PAL experiments and provide recommendations on how to design a PAL probe.

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An electroaffinity labelling platform for chemoproteomic-based target identification

Cited by 18 publications

References 41 publications

Silyl Ether Enables High Coverage Chemoproteomic Interaction Site Mapping

Silyl Ether Enables High Coverage Chemoproteomic Interaction Site Mapping

Application of PROTACs in target identification and validation

Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions

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