Determining cysteines available for covalent inhibition across the human kinome

Zheng Zhao, Qingsong Liu, Spencer Bliven, Lei Xie, and Philip E. Bourne

J. Med. Chem., 2017, 60 (7), pp 2879–2889

DOI: 10.1021/acs.jmedchem.6b01815

Covalently bound protein kinase inhibitors have been frequently designed to target non-catalytic cysteines at the ATP binding site. Thus, it is important to know if a given cysteine can form a covalent bond. Here we combine a function-site interaction fingerprint method and DFT calculations to determine the potential of cysteines to form a covalent interaction with an inhibitor. By harnessing the human structural kinome, a comprehensive structure-based binding site cysteine dataset was assembled. The orientation of the cysteine thiol group indicates which cysteines can potentially form covalent bonds. These covalent inhibitor accessible cysteines are located within five regions: P-loop, roof of pocket, front pocket, catalytic-2 of the catalytic loop and DFG-3 close to the DFG peptide. In an independent test set, these cysteines covered 95% of covalent kinase inhibitors. This study provides new insights into cysteine reactivity and preference which is important for the prospective development of covalent kinase inhibitors.

Specificity of Protein Covalent Modification by the Electrophilic Proteasome Inhibitor Carfilzomib in Human Cells

Joel D. Federspiel, Simona G. Codreanu, Sandeep Goyal, Matthew E. Albertolle, Eric Lowe, Juli Teague, Hansen Wong, F. Peter Guengerich and Daniel C. Liebler

http://www.mcponline.org/content/15/10/3233.short

Ligand and Target Discovery by Fragment-Based Screening in Human Cells

Christopher G. Parker, Andrea Galmozzi, Yujia Wang, Bruno E. Correia, Kenji Sasaki, Christopher M. Joslyn, Arthur S. Kim, Cullen L. Cavallaro, R. Michael Lawrence, Stephen R. Johnson, Iñigo Narvaiza, Enrique Saez, Enrique Saez,Enrique Saez, Benjamin F. Cravatt6, Benjamin F. Cravatt

DOI: 10.1016/j.cell.2016.12.029