• Home
  • Search Results
  • Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.

Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome.

Cell chemical biology (2019-04-16)
Suman Rao, Deepak Gurbani, Guangyan Du, Robert A Everley, Christopher M Browne, Apirat Chaikuad, Li Tan, Martin Schröder, Sudershan Gondi, Scott B Ficarro, Taebo Sim, Nam Doo Kim, Matthew J Berberich, Stefan Knapp, Jarrod A Marto, Kenneth D Westover, Peter K Sorger, Nathanael S Gray
ABSTRACT

Covalent kinase inhibitors, which typically target cysteine residues, represent an important class of clinically relevant compounds. Approximately 215 kinases are known to have potentially targetable cysteines distributed across 18 spatially distinct locations proximal to the ATP-binding pocket. However, only 40 kinases have been covalently targeted, with certain cysteine sites being the primary focus. To address this disparity, we have developed a strategy that combines the use of a multi-targeted acrylamide-modified inhibitor, SM1-71, with a suite of complementary chemoproteomic and cellular approaches to identify additional targetable cysteines. Using this single multi-targeted compound, we successfully identified 23 kinases that are amenable to covalent inhibition including MKNK2, MAP2K1/2/3/4/6/7, GAK, AAK1, BMP2K, MAP3K7, MAPKAPK5, GSK3A/B, MAPK1/3, SRC, YES1, FGFR1, ZAK (MLTK), MAP3K1, LIMK1, and RSK2. The identification of nine of these kinases previously not targeted by a covalent inhibitor increases the number of targetable kinases and highlights opportunities for covalent kinase inhibitor development.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
N,N-Dimethylformamide, anhydrous, 99.8%
Sigma-Aldrich
Triton X-100, laboratory grade
Sigma-Aldrich
Glycerol, for molecular biology, ≥99.0%
Sigma-Aldrich
Trifluoroacetic acid, ReagentPlus®, 99%
Sigma-Aldrich
Tris(2-carboxyethyl)phosphine hydrochloride, powder
Sigma-Aldrich
IGEPAL® CA-630, for molecular biology
Sigma-Aldrich
Sodium acetate, anhydrous, for molecular biology, ≥99%
Sigma-Aldrich
Chloramphenicol, ≥98% (HPLC)
Sigma-Aldrich
d-Desthiobiotin, ≥98% (TLC)
Sigma-Aldrich
Triethylammonium bicarbonate buffer, 1.0 M, pH 8.5±0.1
Sigma-Aldrich
1-Butanol, ACS reagent, ≥99.4%
Sigma-Aldrich
Streptomycin sulfate salt, powder, BioReagent, suitable for cell culture
Sigma-Aldrich
Kanamycin sulfate, mixture of Kanamycin A (main component) and Kanamycin B and C
Sigma-Aldrich
2-Butanol, anhydrous, 99.5%
Sigma-Aldrich
Acryloyl chloride, 97.0%, contains <210 ppm MEHQ as stabilizer
SpeedBeads magnetic carboxylate modified particles, Cytiva 65152105050250, 0.70-1.10 μm avg. part. size, suspension (5% Solids)
Sigma-Aldrich
Benzamidine, ≥95.0%
Sigma-Aldrich
2,4-Dichloropyrimidine, 98%
Sigma-Aldrich
2,4,5-Trichloropyrimidine, 99%
Sigma-Aldrich
5-Iodotubercidin, ≥85%, solid
Sigma-Aldrich
SM1-71-R, ≥98% (HPLC)
Sigma-Aldrich
SM1-71, ≥98% (HPLC)
Supelco
Carbotrap® 400 Dynatherm 890, 850, pkg of 1 ea
Sigma-Aldrich
iTRAQ® Reagents Multiplex Kit