Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• -PAGE) and visualized by in-gel fluorescence scanning (Figure 6A). In this approach the tag is a suitable fluorophore. Previously, during an introduction period of a chemical proteomics workflow of activity-based protein profiling (ABPP), the resulting fluorescent bands might be simply cut out from the

Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• previously described an activity-based protein profiling (ABPP) strategy for NRPSs using ABPs that target A-domains (Figure 2b) [13][14][15]. The probes comprise an aminoacyl-AMS ligand and a photoaffinity group with clickable alkyne functionality appended to the 2′-OH group of adenosine. A complex structure

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• , Cys112, is engaging in the catalytic process forming a covalent reaction intermediate. We thus aimed at exploring the possibility to selectively label the active site cysteine residue using chemical probes. Activity-based protein profiling (ABPP) has become a powerful tool to study protein function and

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• analysis of proteins is the activity-based protein profiling (ABPP) [11][12]. This proteomic strategy uses small probes designed to target active members of enzyme families [13]. These are often based on natural products to investigate their protein targets and eventually their mode of action [14][15

• compares with commercially available azide-modified fluorophores and a brominated one. The ease of synthesis, small size, stability, and the universal detection possibilities make it an ideal reporter for activity-based protein profiling and functional metabolic profiling. Keywords: activity-based protein

• profiling (ABPP); bioorthogonal; click chemistry; mass defect; molecular probe; Introduction Fluorescent dyes are widely used for detection and monitoring in the fields of chemistry, biochemistry, molecular biology, medicine and material sciences. Due to sensitive and selective detection methods and

Design and synthesis of tag-free photoprobes for the identification of the molecular target for CCG-1423, a novel inhibitor of the Rho/MKL1/SRF signaling pathway

• Jessica L. Bell,
• Andrew J. Haak,
• Susan M. Wade,
• Yihan Sun,
• Richard R. Neubig and
• Scott D. Larsen

Beilstein J. Org. Chem. 2013, 9, 966–973, doi:10.3762/bjoc.9.111

• group in performing activity-based protein profiling (ABPP) [19][20]. This entails the incorporation of a ligand for recognition by the target, a reactive functionality for covalently bonding to the target, and either an azide or acetylene moiety as a latent linker for subsequent ligation of a tag for

An improved synthesis of a fluorophosphonate–polyethylene glycol–biotin probe and its use against competitive substrates

• Hao Xu,
• Hairat Sabit,
• Gordon L. Amidon and
• H. D. Hollis Showalter

Beilstein J. Org. Chem. 2013, 9, 89–96, doi:10.3762/bjoc.9.12

• Michigan, Ann Arbor, MI 48109-1065, USA 10.3762/bjoc.9.12 Abstract The fluorophosphonate (FP) moiety attached to a biotin tag is a prototype chemical probe used to quantitatively analyze and enrich active serine hydrolases in complex proteomes in an approach called activity-based protein profiling (ABPP

• biological processes. In this regard, fluorophosphonate (FP) probes have been extensively used in activity-based protein profiling (ABPP) in proteomic studies [1][2]. FP probes, specifically designed to target serine hydrolases, originate from diisopropyl fluorophosphonate (DFP) [3][4]. DFP is a serine