Polyproline-Rod Approach to Isolating Protein Targets of Bioactive Small Molecules:  Isolation of a New Target of Indomethacin

Abstract

Identification of protein targets of bioactive small molecules has been a technical hurdle of chemical genetics. Here we report a polyproline-rod approach to isolating protein targets of small molecules from cell lysates. The results indicate that insertion of a long, rigid polyproline helix between a small-molecule bait and a biotin tag boosts the capacity of affinity purification and thereby permits isolation of low-abundance or low-affinity proteins. In the course of the proof-of-concept experiments, we isolated glyoxalase 1 (GLO1) as a new target of indomethacin, a widely used antiinflammatory drug. Molecular biological experiments suggest that inhibition of GLO1 enzyme activity is related to the clinically recognized beneficial side effects of the indomethacin family of nonsteroidal antiinflammatory drugs.

Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions

“…Simulation results in water appear to be somewhat at variance with the experimental results when DMSO [82] is used as a solvent at the coupling stage during peptoid synthesis but the results were found to be in conformity with the results where DMF has been used as a solvent at the coupling stage between a haloacetic acid and the primary amine of interest. Population of PP-I, inverse PP-I, PP-II and inverse PP-II structures in water is mainly attributed to the formation of hydrogen bonds between peptoid backbone carbonyl oxygens and solvent water molecules.…”

Chemical Biology of Natural Products on the Basis of Identification of Target Proteins

“…Recent progress in chemical biology brings us some promising methods applicable for target ID of NOLs, such as FG-beads technology, 26 photoaffinity beads technology, 27 a fishing-rod strategy, 28 a "compact" molecular probe (CMP) approach, 29 the yeast 3-hybrid (Y3H) system, 30 and a database-dependent (DBD) strategy 31,32 ( Figure 4). Historical background of these techniques can be found in excellent reviews.…”

“…The fishing-rod strategy 28 developed by Uesugi and coworkers ( Figure 4C) employs a unique rigid polyproline linker. Uesugi focused on the 3D structure of the MP to improve its troublesome nature.…”

Medicinal Chemistry and Chemical Biology of Diketopiperazine-Type Antimicrotubule and Vascular-Disrupting Agents

“…44,45) The tubulin photoaffinity labeling study was performed by synthesizing three types of chemical probe. The first chemical probe comprised compound 40 and a biotin tag at the 4-position of the benzophenone ring in 39, and the second chemical probe comprised compound 41 with a linker 46) that was longer than the linker present in 40. The third chemical probe comprised compound 42 with a biotin tag at the 5-position of the oxazole ring (Fig.…”