μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping Article Swipe
YOU?
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· 2023
· Open Access
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· DOI: https://doi.org/10.1021/jacs.3c03325
The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discovery, but in many cases structural characterization is challenging or impossible. PAL has also enabled binding site mapping with peptide- and amino-acid-level resolution; however, the stoichiometric activation mode can lead to poor signal and coverage of the resident binding pocket. Additionally, each PAL probe can have its own fragmentation pattern, complicating the analysis by mass spectrometry. Here, we establish a robust and general photocatalytic approach toward the mapping of protein binding sites, which we define as identification of residues proximal to the ligand binding pocket. By utilizing a catalytic mode of activation, we obtain sets of labeled amino acids in the proximity of the target protein binding site. We use this methodology to map, in vitro, the binding sites of six protein targets, including several kinases and molecular glue targets, and furthermore to investigate the binding site of the STAT3 inhibitor MM-206, a ligand with no known crystal structure. Finally, we demonstrate the successful mapping of drug binding sites in live cells. These results establish μMap as a powerful method for the generation of amino-acid- and peptide-level target engagement data.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/jacs.3c03325
- OA Status
- green
- Cited By
- 54
- References
- 47
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4384925259
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4384925259Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1021/jacs.3c03325Digital Object Identifier
- Title
-
μMap Photoproximity Labeling Enables Small Molecule Binding Site MappingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-07-20Full publication date if available
- Authors
-
Sean W. Huth, James V. Oakley, Ciaran P. Seath, Jacob B. Geri, Aaron Trowbridge, Dann L. Parker, Frances P. Rodriguez‐Rivera, Adam G. Schwaid, Carlo P. Ramil, Keun Ah Ryu, Cory White, Olugbeminiyi Fadeyi, Rob Oslund, David W. C. MacMillanList of authors in order
- Landing page
-
https://doi.org/10.1021/jacs.3c03325Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://pmc.ncbi.nlm.nih.gov/articles/PMC10809032/pdf/nihms-1955484.pdfDirect OA link when available
- Concepts
-
Chemistry, Binding site, Drug discovery, Small molecule, Ligand (biochemistry), Computational biology, Peptide, Amino acid, Target protein, Plasma protein binding, Combinatorial chemistry, Biochemistry, Receptor, Biology, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
54Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 28, 2024: 21, 2023: 5Per-year citation counts (last 5 years)
- References (count)
-
47Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| primary_location.source.host_organization_lineage_names | American Chemical Society |
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| primary_location.raw_source_name | Journal of the American Chemical Society |
| primary_location.landing_page_url | https://doi.org/10.1021/jacs.3c03325 |
| publication_date | 2023-07-20 |
| publication_year | 2023 |
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