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

An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine-56

DOI: 10.1002/anie.201611907 

 The stress-inducible molecular chaperone, HSP72, is an important therapeutic target in oncology, but inhibiting this protein with small molecules has proven particularly challenging. Validating HSP72 inhibitors in cells is difficult owing to competition with the high affinity and abundance of its endogenous nucleotide substrates. We hypothesized this could be overcome using a cysteine-targeted irreversible inhibitor. Using rational design, we adapted a validated 8-N-benzyladenosine ligand for covalent bond formation and confirmed targeted irreversible inhibition. However, no cysteine in the protein was modified; instead, we demonstrate that lysine-56 is the key nucleophilic residue. Targeting this lysine could lead to a new design paradigm for HSP72 chemical probes and drugs.

Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes

Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes

Qian Zhao†‡⊥, Xiaohu Ouyang†⊥, Xiaobo Wan†, Ketan S. Gajiwala∥, John C. Kath∥, Lyn H. Jones§, Alma L. Burlingame‡, and Jack Taunton*†
†Department of Cellular and Molecular Pharmacology and ‡Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
§ Medicine Design, Pfizer, Cambridge, Massachusetts 02139, United States
∥ Worldwide Research and Development, Pfizer, San Diego, California 92121, United States
J. Am. Chem. Soc., 2017, 139 (2), pp 680–685
DOI: 10.1021/jacs.6b08536
Publication Date (Web): January 4, 2017
Copyright © 2017 American Chemical Society

Covalent Modulators of the Vacuolar ATPase

Ying-Chu Chen, Keriann M. Backus, Maria Merkulova, Christina Yang, Dennis Brown, Benjamin F. Cravatt, and Chao Zhang

J. Am. Chem. Soc., 2017, 139 (2), pp 639–642

DOI: 10.1021/jacs.6b12511

What Do Reactive Fragments Actually Do in Cells?

What Do Reactive Fragments Actually Do in Cells?
Angewante Chemie
Prof. Dr. Oliver Plettenburg
DOI: 10.1002/anie.201607914