title: Benzimidazole covalent probes and the gastric H(+)/K(+)-ATPase as a model system for protein labeling in a copper-free setting.
abstract: Affinity probes are useful tools for determining molecular targets and elucidating mechanism of action for novel, bioactive compounds. In the case of covalent inhibitors, activity based probes are particularly valuable for ensuring acceptable selectivity margins. However, there is a variety of bioorthogonal chemistry reactions available for modifying compounds of interest with clickable tags. Here, we describe a direct comparison of tetrazine ligation and strain promoted azide-alkyne cycloaddition using benzimidazole based probes to bind their known target, the gastric proton pump, ATP4A. This study validates the use of chemical probes for target identification and illustrates the superior efficiency of tetrazine ligation for copper-free click systems. In addition, we have identified several novel binding partners of benzimidazole probes: Isoform 2 of deleted in malignant brain tumors 1 protein (DMBT1) and three uncharacterized proteins.
authors.affiliation: Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. liy2@mskcc.org and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
authors.forename: Chelsea J
authors.initials: CJ
authors.lastname: Paresi
authors.affiliation: Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. liy2@mskcc.org.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. liy2@mskcc.org and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.
authors.forename: Yue-Ming
authors.initials: YM
authors.lastname: Li
mesh_terms: D001562:Benzimidazoles / Q000138:chemical synthesis / Q000737:chemistry*; D003300:Copper / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry; D017506:H(+)-K(+)-Exchanging ATPase / Q000737:chemistry* / Q000378:metabolism*; D013058:Mass Spectrometry; D008856:Microscopy, Fluorescence; D015335:Molecular Probes / Q000138:chemical synthesis / Q000737:chemistry*; D015394:Molecular Structure; D054328:Proton Pump Inhibitors / Q000138:chemical synthesis / Q000737:chemistry*; D013194:Staining and Labeling
chemical_list: D001562:Benzimidazoles; D005456:Fluorescent Dyes; D015335:Molecular Probes; D054328:Proton Pump Inhibitors; D003300:Copper; C031000:benzimidazole; D017506:H(+)-K(+)-Exchanging ATPase